bluuebunny/crossref_metadata_2025_split huggingface dataset:
State and green crimes related to water pollution and ecological disorganization: water pollution from publicly owned treatment works (POTW) facilities across US states
Authors: Lynch Michael J. , Stretesky Paul B. , Long Michael A. 
Published: August 2017

AbstractGreen criminologists often refer to water pollution as an example of a green crime, but have yet to produce much research on this subject. The current article addresses the need for green criminological analyses of water pollution problems, and draws attention to an overlooked issue: water pollution emissions from state owned public water treatment facilities or POTWs. Legally, POTWs may emit certain quantities and kinds of pollutants to waterways following treatment. This does not mean, however, that those emissions have no adverse ecological or public health impacts, or that those emissions cannot also be employed as examples of green crimes or green-state crimes. Indeed, from the perspective of environmental sociology and ecological Marxism, those emissions generate ecological disorganization. Moreover, POTW emissions contain numerous pollutants that generate different forms of ecological disorganization. The current study uses POTW emissions data drawn from the US EPA’s Discharge Monitoring Report system for 2014 to illustrate the extent of pollution emitted by POTWs in and across US states as one dimension of ecological disorganization. To contextualize the meaning of those data, we review US water pollution regulations, review the health and ecological impacts of chemicals emitted by POTWs, and situate those emissions within green criminological discussions of green crime and green-state crimes.
The unemployable and the generic: rethinking the commons in the communist hypothesis
Authors: Tupinambá Gabriel 
Published: August 2017

AbstractOne of the main points of contention in the current debates surrounding Marxism has been the problem of finding a concrete substrate, which would orient the recuperation of the communist political strategy. Are there impasses in our contemporary society which justify the use of such a polemical notion as communism? Most authors currently involved with this debate agree that it is the problem of the “commons" under capitalism, which calls for a new theory and practice of communism. Where they disagree is on what the “commons” are and on how they exist within capitalism itself. The present contribution seeks to intervene on this debate and spell out the categorial recomposition of some fundamental aspects of Marxist critique of political economy implicitly at stake in Slavoj Žižek’s theorization of the “antagonisms of the common”. Taking up the insight of Antonio Negri and Michael Hardt concerning the new centrality of the enclosure of the commons in contemporary capitalism, Žižek has developed an alternative—more sober—view of the structural subsumption of these common spaces to the dynamics of Capital, where the very communal dimension of these domains only appear as common after they have been privatized. To extract the consequences of this assertion, we will first reconstruct the Marxist theory of enclosures in a comparative reading of the first volume of Capital and Karl Polanyi’s classic The Great Transformation. This will lead us to a broader discussion of the contemporary transformations in capitalism, with a focus on the crisis of value as primarily sustained by absolute surplus-value extraction. With an understanding of the idea of the commons and a historical background of our current predicament, we will be in position to follow Antonio Negri’s reading of how the enclosure of the commons leads to a new communist strategy and also to criticize it, using Slavoj Zizek’s alternative understanding of our contemporary social antagonisms. Following through Zizek's reading of the logic of enclosures, we come to the conclusion that, first, unemployment has the structure of an enclosure, one which is responsible for the very form of the work commodity—as it was already suggested by Fredric Jameson and others—and, second, that, from a certain philosophical perspective shared by thinkers such as Zizek and Badiou, this realization can lead us to an innovative recuperation of the Marxist theory of “generic being”, proposed by Marx in his Manuscripts of 1844.
Empirical prediction intervals improve energy forecasting
Authors: Kaack Lynn H. , Apt Jay , Morgan M. Granger , McSharry Patrick 
Published: August 2017

Significance
While many forecasters are moving toward generating probabilistic predictions, energy forecasts typically still consist of point projections and scenarios without associated probabilities. Empirical density forecasting methods provide a probabilistic amendment to existing point forecasts. Here we lay the groundwork for evaluating the performance of these methods in the data-scarce setting of long-term forecasts. Results can give policy analysts and other users confidence in estimating forecast uncertainties with empirical methods.
Metal-mediated diradical tuning for DNA replication arrest via template strand scission
Authors: Porter Meghan R. , Lindahl Sarah E. , Lietzke Anne , Metzger Erin M. , Wang Quan , Henck Erik , Chen Chun-Hsing , Niu Hengyao , Zaleski Jeffrey M. 
Published: August 2017

SignificancePharmaceuticals often act within a lock-and-key model whereby molecules bind their targets nearly irreversibly, either stalling or initiating biological processes. Here, the agent itself performs no chemical transformation on its target but rather triggers an event or cascade. However, unwanted side effects become more likely as the reactivity of these molecules increases. In contrast, molecular compounds may irreversibly damage biological targets using metal-mediated radical chemistry, but controlling the onset and extent of reaction is challenging. Even so, multiple examples of metal-containing or metal-radical paradigms have been used clinically for imaging and chemotherapy. Within this framework we report a class of metal-mediated radical generators that attack DNA, outcompete DNA polymerase, and are cytotoxic in short times and modest concentrations.
Factor-dependent archaeal transcription termination
Authors: Walker Julie E. , Luyties Olivia , Santangelo Thomas J. 
Published: August 2017

Significance
Proper transcription regulation is necessary for timely and accurate gene expression underlying growth and development. Transcription is regulated at each stage of the transcription cycle—initiation, elongation, and termination—and it is critical to define the factors and sequences regulating RNA polymerase activity. Many studies have investigated the mechanisms used by transcription factors involved in regulation of transcription initiation and elongation, but a mechanistic understanding of transcription termination has been slower to emerge. Here we characterize the first archaeal transcription termination factor, termed euryarchaeal termination activity (Eta). The mechanisms of Eta-mediated termination provide the first understanding of archaeal factor-dependent termination and provide insight into and contrast with the mechanisms used for factor-dependent termination in extant life.
Atypical fracture with long-term bisphosphonate therapy is associated with altered cortical composition and reduced fracture resistance
Authors: Lloyd Ashley A. , Gludovatz Bernd , Riedel Christoph , Luengo Emma A. , Saiyed Rehan , Marty Eric , Lorich Dean G. , Lane Joseph M. , Ritchie Robert O. , Busse Björn , Donnelly Eve 
Published: August 2017

Significance
Since the first reports of atypical femoral fractures (AFFs), a clinical phenomenon in which patients experience catastrophic brittle fractures of the femoral shaft with minimal trauma, the risk associated with bisphosphonates, the most widely prescribed pharmaceuticals for osteoporosis, has become increasingly well-established. However, the underlying cause of AFFs and their causal relationship to bisphosphonates is unknown. Here we examine bone tissue from women with AFFs and show that long-term bisphosphonate treatment degrades the fracture-resistance toughening mechanisms that are inherent to healthy bone. Our work resolves the apparent paradox of AFFs as a side effect of the most common osteoporosis treatment by clarifying the differing effects of bisphosphonates on bone tissue structure and mechanical properties across multiple length scales.
PUM1 is a biphasic negative regulator of innate immunity genes by suppressing LGP2
Authors: Liu Yonghong , Qu Linlin , Liu Yuanyuan , Roizman Bernard , Zhou Grace Guoying 
Published: August 2017

Significance
We report that PUM1, a protein linked to control of translation of mRNAs carrying a cognate sequence, is a negative regulator of LGP2. In turn LGP2 emerged as a biphasic master activator of numerous innate immunity genes leading to production of interferon. The studies traced in real-time the changes in innate immune responses following transfection of siPUM1 RNA. This approach enabled the discovery that innate immune genes analyzed in this report were activated sequentially in a cascade fashion. The studies were done in uninfected cells in the absence of viral gene products that could affect the expression of cellular genes. This report seeds the possibility of systemic engagement of innate immune responses following life-threatening viral infections by suppressing PUM1 function.
Habitat Use by Telemetered Alabama Shad During the Spawning Migration in the Lower Flint River, Georgia
Authors: Kern A. I. , Sammons S. M. , Ingram T. R. 
Published: August 2017

Abstract
The Alabama Shad Alosa alabamae is an anadromous clupeid that lives in the northern Gulf of Mexico and ascends freshwater rivers in spring to spawn. Populations have experienced substantial range-wide declines due to habitat alteration. The largest known population of Alabama Shad is found in the Apalachicola River in northwest Florida. To assess their movement during the spawning migration, 250 Alabama Shad were fitted with acoustic or radio transmitters, depending on year, and transported upstream from Jim Woodruff Lock and Dam during 2010–2014. The 153 relocations from 126 individual fish revealed congregation areas that were suspected to be spawning locations. Alabama Shad selected limerock boulder substrate, avoided limerock fine and rocky substrates and used sandy substrate in the same proportion as its availability. Alabama Shad upstream movement was greatest during April through mid-May. Movements ≥ 20 km were generally clustered together over a period of a few days, with ~90% of such movements occurring following periods of increased river discharge. All limerock boulder substrate areas on the lower Flint River were identified to focus future efforts to determine exact spawning locations.
Consumers’ Willingness to Pay for Health Benefits in Food Products: A Meta‐Analysis
Authors: Dolgopolova Irina , Teuber Ramona 
Published: August 2017

AbstractThis article analyzes the existing literature on consumers’ marginal willingness to pay (MWTP) for health benefits in food products. Results indicate that the presence of a health claim does not only increase MWTP for health benefits in foods but also reduces heterogeneity among MWTP estimates. Hypothetical methods significantly positively affect MWTP. The most popular product category “dairy” negatively influences MWTP. The popular health claim of “lowering cholesterol” has a significantly positive influence on MWTP. In addition, our review highlights that existing studies significantly differ in their setup, which renders the inference of clear‐cut conclusions rather problematic.
LRCstats, a tool for evaluating long reads correction methods
Authors: La Sean , Haghshenas Ehsan , Chauve Cedric 
Published: August 2017

Abstract

Motivation
Third-generation sequencing (TGS) platforms that generate long reads, such as PacBio and Oxford Nanopore technologies, have had a dramatic impact on genomics research. However, despite recent improvements, TGS reads suffer from high-error rates and the development of read correction methods is an active field of research. This motivates the need to develop tools that can evaluate the accuracy of noisy long reads correction tools.

Results
We introduce LRCstats, a tool that measures the accuracy of long reads correction tools. LRCstats takes advantage of long reads simulators that provide each simulated read with an alignment to the reference genome segment they originate from, and does not rely on a step of mapping corrected reads onto the reference genome. This allows for the measurement of the accuracy of the correction while being consistent with the actual errors introduced in the simulation process used to generate noisy reads. We illustrate the usefulness of LRCstats by analyzing the accuracy of four hybrid correction methods for PacBio long reads over three datasets.

Availability and implementation
https://github.com/cchauve/lrcstats

Supplementary information
Supplementary data are available at Bioinformatics online.
DIMM-SC: a Dirichlet mixture model for clustering droplet-based single cell transcriptomic data
Authors: Sun Zhe , Wang Ting , Deng Ke , Wang Xiao-Feng , Lafyatis Robert , Ding Ying , Hu Ming , Chen Wei 
Published: August 2017

AbstractMotivationSingle cell transcriptome sequencing (scRNA-Seq) has become a revolutionary tool to study cellular and molecular processes at single cell resolution. Among existing technologies, the recently developed droplet-based platform enables efficient parallel processing of thousands of single cells with direct counting of transcript copies using Unique Molecular Identifier (UMI). Despite the technology advances, statistical methods and computational tools are still lacking for analyzing droplet-based scRNA-Seq data. Particularly, model-based approaches for clustering large-scale single cell transcriptomic data are still under-explored.ResultsWe developed DIMM-SC, a Dirichlet Mixture Model for clustering droplet-based Single Cell transcriptomic data. This approach explicitly models UMI count data from scRNA-Seq experiments and characterizes variations across different cell clusters via a Dirichlet mixture prior. We performed comprehensive simulations to evaluate DIMM-SC and compared it with existing clustering methods such as K-means, CellTree and Seurat. In addition, we analyzed public scRNA-Seq datasets with known cluster labels and in-house scRNA-Seq datasets from a study of systemic sclerosis with prior biological knowledge to benchmark and validate DIMM-SC. Both simulation studies and real data applications demonstrated that overall, DIMM-SC achieves substantially improved clustering accuracy and much lower clustering variability compared to other existing clustering methods. More importantly, as a model-based approach, DIMM-SC is able to quantify the clustering uncertainty for each single cell, facilitating rigorous statistical inference and biological interpretations, which are typically unavailable from existing clustering methods.Availability and implementationDIMM-SC has been implemented in a user-friendly R package with a detailed tutorial available on www.pitt.edu/∼wec47/singlecell.html.Supplementary informationSupplementary data are available at Bioinformatics online.
ComplexViewer: visualization of curated macromolecular complexes
Authors: Combe Colin W , Sivade Marine (Dumousseau) , Hermjakob Henning , Heimbach Joshua , Meldal Birgit H M , Micklem Gos , Orchard Sandra , Rappsilber Juri 
Published: August 2017

Abstract

Summary
Proteins frequently function as parts of complexes, assemblages of multiple proteins and other biomolecules, yet network visualizations usually only show proteins as parts of binary interactions. ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions. Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex.

Availability and implementation
freely available under Apache version 2 license; EMBL-EBI Complex Portal: http://www.ebi.ac.uk/complexportal; Source code: https://github.com/MICommunity/ComplexViewer; Package: https://www.npmjs.com/package/complexviewer; http://biojs.io/d/complexviewer. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js.
Motif independent identification of potential RNA G-quadruplexes by G4RNA screener
Authors: Garant Jean-Michel , Perreault Jean-Pierre , Scott Michelle S 
Published: August 2017

Abstract

Motivation
G-quadruplex structures in RNA molecules are known to have regulatory impacts in cells but are difficult to locate in the genome. The minimal requirements for G-quadruplex folding in RNA (G≥3N1-7 G≥3N1-7 G≥3N1-7 G≥3) is being challenged by observations made on specific examples in recent years. The definition of potential G-quadruplex sequences has major repercussions on the observation of the structure since it introduces a bias. The canonical motif only describes a sub-population of the reported G-quadruplexes. To address these issues, we propose an RNA G-quadruplex prediction strategy that does not rely on a motif definition.

Results
We trained an artificial neural network with sequences of experimentally validated G-quadruplexes from the G4RNA database encoded using an abstract definition of their sequence. This artificial neural network, G4NN, evaluates the similarity of a given sequence to known G-quadruplexes and reports it as a score. G4NN has a predictive power comparable to the reported G richness and G/C skewness evaluations that are the current state-of-the-art for the identification of potential RNA G-quadruplexes. We combined these approaches in the G4RNA screener, a program designed to manage and evaluate the sequences to identify potential G-quadruplexes.

Availability and implementation
G4RNA screener is available for download at http://gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener.

Supplementary information
Supplementary data are available at Bioinformatics online.
‘A woman’s place…’: community-based approaches to gender-based violence in Malawi
Authors: Gaynor Niamh , Cronin Máirtín 
Published: August 2017

Abstract
One in five women has experienced gender-based violence (GBV) in Malawi and its incidence is reported to be increasing. The importance of cultural norms, practices, discourses and behaviours in both driving and addressing such violence is now well recognized. So too is the attendant need to involve men as well as women in community interventions to address this. In this context, this article draws on field research conducted in 2016 in two districts in Northern and Southern Malawi exploring the successes and challenges posed by community-based approaches (CBAs) to tackling GBV. We find that CBAs have yielded a number of successes – notably a reported reduction in GBV as communications between couples have improved and economic stresses within households reduced. However, we also find that these same CBAs have raised a number of challenges. These centre around resource distribution; the impact on local power dynamics; and CBA’s ability to challenge and interrogate dominant norms, ideologies, identities and practices. Overall, we argue that, while CBAs appear successful in transmitting the message to both women and men that GBV is unlawful and wrong, their impacts on the principal underlying causal factors remain weak.
Assessment of Efficacy and Safety of Arterolane Maleate–Piperaquine Phosphate Dispersible Tablets in Comparison With Artemether-Lumefantrine Dispersible Tablets in Pediatric Patients With Acute Uncomplicated Plasmodium falciparum Malaria: A Phase 3, Randomized, Multicenter Trial in India and Africa
Authors: Toure Offianan Andre , Mwapasa Victor , Sagara Issaka , Gaye Oumar , Thompson Ricardo , Maheshwar Aishwarya V , Mishra Pitabas , Behra Narendra , Tshefu Antoinette K , Das Rashmi R , Anvikar Anupkumar R , Sharma Pradeep , Roy Arjun , Sharma Sanjay K , Nasa Amit , Jalali Rajinder K , Valecha Neena ,   for the Arterolane Maleate-Piperaquine Phosphate (AM-PQP) Study Team, Beatrice Toure N , Valery Kouame N’Goran , Karim Tuo , Tiacoh Landry , Kigninma Ouattara , Sibale Naomi , Kaneka Kelvin , Machilika Mercy , Mabote Sheila , Bonzela Juvencio , Lourenceo Carlos , Dieudonneée Bidashimwa , Kasonga Paulin , Ndiaye Jean-Louis , Diop Modou , Sidibe Bouran , Coulibaly Moctar , Fofana Bakary , Toure Sekou , Panigrahy Ankita , Patro Debasis , Biswas Tapan Kumar , Panigrahy Preetish Kumar , Jana Saibal , Hota Debasish , Behera Bijayini , Mohanty Akshaya , Patel Goutam 
Published: August 2017

Abstract

Background
Administration of artemisinin-based combination therapy (ACT) to infant and young children can be challenging. A formulation with accurate dose and ease of administration will improve adherence and compliance in children. The fixed-dose combination dispersible tablet of arterolane maleate (AM) 37.5 mg and piperaquine phosphate (PQP) 187.5 mg can make dosing convenient in children.

Methods
This multicenter (India and Africa), comparative, parallel-group trial enrolled 859 patients aged 6 months to 12 years with Plasmodium falciparum malaria. Patients were randomized in a ratio of 2:1 to AM-PQP (571 patients) once daily and artemether-lumefantrine (AL) (288 patients) twice daily for 3 days and followed for 42 days.

Results
The cure rate (ie, polymerase chain reaction–corrected adequate clinical and parasitological response) in the per-protocol population at day 28 was 100.0% and 98.5% (difference, 1.48% [95% confidence interval {CI}, .04%–2.91%]) in the AM-PQP and AL arms, respectively, and 96.0% and 95.8% (difference, 0.14% [95% CI, –2.68% to 2.95%]) in the intention-to-treat (ITT) population. The cure rate was comparable at day 42 in the ITT population (AM-PQP, 94.4% vs AL, 93.1%). The median parasite clearance time was 24 hours in both the arms. The median fever clearance time was 6 hours in AM-PQP and 12 hours in the AL arm. Both the treatments were found to be safe and well tolerated. Overall, safety profile of both the treatments was similar.

Conclusions
The efficacy and safety of fixed-dose combination of AM and PQP was comparable to AL for the treatment of uncomplicated P. falciparum malaria in pediatric patients.

Clinical Trials Registration
CTRI/2014/07/004764.