bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agricultural Water Allocation under Uncertainty: Redistribution of Water Shortage Risk
Authors: Li Man , Xu Wenchao , Zhu Tingju 
Published: June 2018

AbstractThis article develops an economic model to analyze how the risk of water shortages affects farmers’ land irrigation decision and how the priority‐based water sharing arrangement redistributes such a risk among farms with different water rights priorities. The analysis brings together an array of comprehensive data files on irrigation rights, water supplies, and agricultural land use from eastern Idaho. Results indicate that a more left‐skewed distribution of streamflow significantly discourages land irrigation among farmers except the most senior rights holders. The priority‐based water sharing arrangement redistributes the macroscale risk of water shortages and thus exposes farmers of different water rights priorities to heterogeneous levels of risk: senior water rights holders are affected the least and such a risk is instead passed mostly on to junior water rights holders. The role of water rights in risk redistribution is more significant when the probability distribution of water shortage risk is asymmetric rather than symmetric. The historical development pattern of water rights influences how the priority of water rights takes effect on land irrigation decision.
NeoDTI: neural integration of neighbor information from a heterogeneous network for discovering new drug–target interactions
Authors: Wan Fangping , Hong Lixiang , Xiao An , Jiang Tao , Zeng Jianyang 
Published: June 2018

Abstract

Motivation
Accurately predicting drug–target interactions (DTIs) in silico can guide the drug discovery process and thus facilitate drug development. Computational approaches for DTI prediction that adopt the systems biology perspective generally exploit the rationale that the properties of drugs and targets can be characterized by their functional roles in biological networks.

Results
Inspired by recent advance of information passing and aggregation techniques that generalize the convolution neural networks to mine large-scale graph data and greatly improve the performance of many network-related prediction tasks, we develop a new nonlinear end-to-end learning model, called NeoDTI, that integrates diverse information from heterogeneous network data and automatically learns topology-preserving representations of drugs and targets to facilitate DTI prediction. The substantial prediction performance improvement over other state-of-the-art DTI prediction methods as well as several novel predicted DTIs with evidence supports from previous studies have demonstrated the superior predictive power of NeoDTI. In addition, NeoDTI is robust against a wide range of choices of hyperparameters and is ready to integrate more drug and target related information (e.g. compound–protein binding affinity data). All these results suggest that NeoDTI can offer a powerful and robust tool for drug development and drug repositioning.

Availability and implementation
The source code and data used in NeoDTI are available at: https://github.com/FangpingWan/NeoDTI.

Supplementary information
Supplementary data are available at Bioinformatics online.
lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data
Authors: Haghshenas Ehsan , Sahinalp S Cenk , Hach Faraz 
Published: June 2018

Abstract

Motivation
Recent advances in genomics and precision medicine have been made possible through the application of high throughput sequencing (HTS) to large collections of human genomes. Although HTS technologies have proven their use in cataloging human genome variation, computational analysis of the data they generate is still far from being perfect. The main limitation of Illumina and other popular sequencing technologies is their short read length relative to the lengths of (common) genomic repeats. Newer (single molecule sequencing – SMS) technologies such as Pacific Biosciences and Oxford Nanopore are producing longer reads, making it theoretically possible to overcome the difficulties imposed by repeat regions. Unfortunately, because of their high sequencing error rate, reads generated by these technologies are very difficult to work with and cannot be used in many of the standard downstream analysis pipelines. Note that it is not only difficult to find the correct mapping locations of such reads in a reference genome, but also to establish their correct alignment so as to differentiate sequencing errors from real genomic variants. Furthermore, especially since newer SMS instruments provide higher throughput, mapping and alignment need to be performed much faster than before, maintaining high sensitivity.

Results
We introduce lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

Availability and implementation
lordFAST is implemented in C++ and supports multi-threading. The source code of lordFAST is available at https://github.com/vpc-ccg/lordfast.

Supplementary information
Supplementary data are available at Bioinformatics online.
emeraLD: rapid linkage disequilibrium estimation with massive datasets
Authors: Quick Corbin , Fuchsberger Christian , Taliun Daniel , Abecasis Gonçalo , Boehnke Michael , Kang Hyun Min 
Published: June 2018

Abstract

Summary
Estimating linkage disequilibrium (LD) is essential for a wide range of summary statistics-based association methods for genome-wide association studies. Large genetic datasets, e.g. the TOPMed WGS project and UK Biobank, enable more accurate and comprehensive LD estimates, but increase the computational burden of LD estimation. Here, we describe emeraLD (Efficient Methods for Estimation and Random Access of LD), a computational tool that leverages sparsity and haplotype structure to estimate LD up to 2 orders of magnitude faster than current tools.

Availability and implementation
emeraLD is implemented in C++, and is open source under GPLv3. Source code and documentation are freely available at http://github.com/statgen/emeraLD.

Supplementary information
Supplementary data are available at Bioinformatics online.
A maximum likelihood approach to power calculations for stepped wedge designs of binary outcomes
Authors: Zhou Xin , Liao Xiaomei , Kunz Lauren M , Normand Sharon-Lise T , Wang Molin , Spiegelman Donna 
Published: June 2018

Summary
In stepped wedge designs (SWD), clusters are randomized to the time period during which new patients will receive the intervention under study in a sequential rollout over time. By the study’s end, patients at all clusters receive the intervention, eliminating ethical concerns related to withholding potentially efficacious treatments. This is a practical option in many large-scale public health implementation settings. Little statistical theory for these designs exists for binary outcomes. To address this, we utilized a maximum likelihood approach and developed numerical methods to determine the asymptotic power of the SWD for binary outcomes. We studied how the power of a SWD for detecting risk differences varies as a function of the number of clusters, cluster size, the baseline risk, the intervention effect, the intra-cluster correlation coefficient, and the time effect. We studied the robustness of power to the assumed form of the distribution of the cluster random effects, as well as how power is affected by variable cluster size. % SWD power is sensitive to neither, in contrast to the parallel cluster randomized design which is highly sensitive to variable cluster size. We also found that the approximate weighted least square approach of Hussey and Hughes (2007, Design and analysis of stepped wedge cluster randomized trials. Contemporary Clinical Trials 28, 182–191) for binary outcomes under-estimates the power in some regions of the parameter spaces, and over-estimates it in others. The new method was applied to the design of a large-scale intervention program on post-partum intra-uterine device insertion services for preventing unintended pregnancy in the first 1.5 years following childbirth in Tanzania, where it was found that the previously available method under-estimated the power.
Causal inference in continuous time: an example on prostate cancer therapy
Authors: Ryalen Pål Christie , Stensrud Mats Julius , Fosså Sophie , Røysland Kjetil 
Published: June 2018

Abstract
In marginal structural models (MSMs), time is traditionally treated as a discrete parameter. In survival analysis on the other hand, we study processes that develop in continuous time. Therefore, Røysland (2011. A martingale approach to continuous-time marginal structural models. Bernoulli 17, 895–915) developed the continuous-time MSMs, along with continuous-time weights. The continuous-time weights are conceptually similar to the inverse probability weights that are used in discrete time MSMs. Here, we demonstrate that continuous-time MSMs may be used in practice. First, we briefly describe the causal model assumptions using counting process notation, and we suggest how causal effect estimates can be derived by calculating continuous-time weights. Then, we describe how additive hazard models can be used to find such effect estimates. Finally, we apply this strategy to compare medium to long-term differences between the two prostate cancer treatments radical prostatectomy and radiation therapy, using data from the Norwegian Cancer Registry. In contrast to the results of a naive analysis, we find that the marginal cumulative incidence of treatment failure is similar between the strategies, accounting for the competing risk of other death.
Emerging from the reds, greens and stripped screws: a communal healing process
Authors: van der Watt Phia 
Published: June 2018

AbstractThe article posits that the field of community development does not adequately engage with intergenerational communal wounding. A family support programme, developed in vulnerable communities in South Africa, was used as case study to investigate the feasibility of healing within community development. The articulation of a clear storyline to guide the process was identified as critical. The programme’s storyline unfolded in four episodes: facing the past (reds and greens); exploring current manifestations thereof (labels, secrets, obscured desires and projections); naming debilitating problems (the screws) to elicit a yearning for healing and action and creating new life stories. Reflection and mirroring through group work were identified as critical elements in this approach. The study concludes that while participants originally accepted the (false) messages/images resulting from oppression and discrimination uncritically, a more authentic self gradually emerged, which directed transformative action (underscoring the Freirean concept of conscientisation). The study invites further debate/research on issues, such as personal healing within group context; the dilemma of risk-and-failure; the slow nature of healing versus organisational demands; and the balance between promises for material improvement and healing. The study shows that communal healing work is both feasible and critically needed within the community development context and offers a practical way to realise this.
Synaptic Mechanisms for Bandwidth Tuning in Awake Mouse Primary Auditory Cortex
Authors: Li Haifu , Liang Feixue , Zhong Wen , Yan Linqing , Mesik Lucas , Xiao Zhongju , Tao Huizhong W , Zhang Li I 
Published: June 2018

AbstractSpatial size tuning in the visual cortex has been considered as an important neuronal functional property for sensory perception. However, an analogous mechanism in the auditory system has remained controversial. In the present study, cell-attached recordings in the primary auditory cortex (A1) of awake mice revealed that excitatory neurons can be categorized into three types according to their bandwidth tuning profiles in response to band-passed noise (BPN) stimuli: nonmonotonic (NM), flat, and monotonic, with the latter two considered as non-tuned for bandwidth. The prevalence of bandwidth-tuned (i.e., NM) neurons increases significantly from layer 4 to layer 2/3. With sequential cell-attached and whole-cell voltage-clamp recordings from the same neurons, we found that the bandwidth preference of excitatory neurons is largely determined by the excitatory synaptic input they receive, and that the bandwidth selectivity is further enhanced by flatly tuned inhibition observed in all cells. The latter can be attributed at least partially to the flat tuning of parvalbumin inhibitory neurons. The tuning of auditory cortical neurons for bandwidth of BPN may contribute to the processing of complex sounds.
The structure of a recent nova shell as observed by ALMA
Authors: Diaz Marcos P , Abraham Zulema , Ribeiro Valério A R M , Beaklini Pedro P B , Takeda Larissa 
Published: June 2018

ABSTRACT
High resolution ALMA observations of the recent (2.52 yr old) shell of Nova V5668 Sgr (2015) show a highly structured ionized gas distribution with small (1015 cm) clumps. These are the smallest structures ever observed in the remnant of a stellar thermonuclear explosion. No extended contiguous emission could be found above the 2.5σ level in our data, while the peak hydrogen densities in the clumps reach 106 cm−3. The millimetre continuum image suggests that large scale structures previously distinguished in other recent nova shells may result from the distribution of bright unresolved condensations.
Arabic Dialectology
Authors: Behnstedt Peter , Woidich Manfred 
Published: June 2018

AbstractGeographically, Arabic is one of the most widespread languages of the world, and Arabic dialects are spoken in an unbroken expanse from western Iran to Mauritania and Morocco and from Oman to northeastern Nigeria, albeit with vast uninhabited or scarcely inhabited areas and deserts in between. It is not easy to give the exact number of speakers, estimates from 1999 (i.e., from eighteen years ago) count 206 million L1 speakers, a figure which today seems too low rather than too high.1 This geographical range is marked by extreme dialectal differences in all fields of phonology, grammar, and lexicon, at times to the extent that different varieties are mutually unintelligible.
The Hostile Media Effect
Authors: Feldman Lauren 
Published: June 2018

Abstract
The “hostile media effect” occurs when opposing partisans perceive identical news coverage of a controversial issue as biased against their own side. This is a robust phenomenon, which has been empirically demonstrated in numerous experimental and observational studies across a variety of issue contexts and has been shown to have important consequences for democratic society. This chapter reviews the literature on the hostile media effect with an eye toward the theoretical explanations for it, its relationship to other psychological processes, and its broader implications for perceived public opinion, news consumption patterns, attitudes toward democratic institutions, and political discourse and participation. Particular attention is paid to how the hostile media phenomenon can help explain the public’s eroding trust in the news media and the recent polarization among news audiences. The chapter concludes with several suggestions for future research.
Online News Consumption in the United States and Ideological Extremism
Authors: Winneg Kenneth M. , Butler Daniel M. , Golde Saar , Miller Darwin W. , Nie Norman H. 
Published: June 2018

Abstract
In an earlier study, the authors found evidence that supported a framework predicting that consumers of Internet news sources held more extreme political views and were interested in more diverse political issues than those who solely consume mainstream television news using data covering the period April 2000 to June 2007. In this essay, they test whether the same patterns hold using data from the 2008 National Annenberg Election Survey online panel conducted during the 2008 presidential election cycle. The authors combine insights from theories of selective media exposure from political communication and social psychology with economic theories of differentiated products markets to develop a theoretical framework for understanding how the Internet continues to impact the U.S. political news market. The driving force behind this framework is the dramatically lower cost of production for Internet news sources relative to traditional television news.
Theories and Effects of Political Humor
Authors: Young Dannagal G. 
Published: June 2018

Abstract
As both an art form and a mode of persuasive discourse, the use of political humor dates back to ancient Greece and Rome. For centuries politicians, citizens, and elites have marveled at and even feared its powerful—and magical—influence on public opinion. By reflecting on various approaches to the study of political humor’s content, audience, and impact, this chapter offers scholars multiple ways to consider the effects of political humor on individuals and society. It culminates with a consideration of the latest advances in the study of political humor and humor theory and poses challenges to those in the field to better explicate micro-level processes that incorporate structural elements of the text and characteristics of the audience.
Theories of Media Bias
Authors: Lichter S. Robert 
Published: June 2018

Abstract
Ideological or partisan media bias is widely debated despite disagreement about its meaning, measurement, and impact. The assumption that news should be objective is itself the object of considerable debate. Assertions of a conservative or establishment bias in the news often draw on critical theory, which argues that news preserves the hegemony of society’s ruling interests. Assertions of liberal bias draw on surveys of journalists’ attitudes and content analyses of news coverage. This case has recently been bolstered by economic modeling. However, numerous content analytic studies have failed to find a liberal bias. This has led to efforts to explain public perceptions of liberal bias in terms of cognitive psychology and elite manipulation. Other explanations include structural biases and media negativism. Internet-driven changes in journalism, including an increase in partisan news, may force a rethinking of the entire debate or even render it irrelevant.
Public and Elite Perceptions of News Media in Politics
Authors: Tsfati Yariv 
Published: June 2018

Abstract
This chapter provides an overview of the research on individual’s perceptions about and attitudes toward the news media. It discusses research on trust in media, hostile media perceptions, and perceptions of media influence, also known as third person perceptions. All three perceptions are shaped by both cognitive and self-enhancement mechanisms and all have important political consequences. The chapter argues that perceptions about the news media among the elite have largely been ignored by scholars but are consequential in shaping the political world. When politicians perceive that media are powerful, they react by initiating coverage and cooperating with the requests of journalists. When a certain issue is expected to receive substantial media attention, politicians react by initiating legislation or discussion about that topic. Thus, politicians’ perceptions of media the may be at the heart of a decades-long process of mediatization of politics.
Classic SRY‐box protein SOX7 functions as a tumor suppressor regulating WNT signaling and is methylated in renal cell carcinoma
Authors: Wang Lu , Fan Yu , Zhang Lian , Li Lili , Kuang Guanyu , Luo Cheng , Li Chen , Xiang Tingxiu , Tao Qian , Zhang Qian , Ying Jianming 
Published: June 2018

ABSTRACTSOX7 (SRY‐related high mobility group box 7), a high mobility group protein, is reported to be down‐regulated in several cancer types, which indicates an important role in tumorigenesis; however, its biologic role in renal cell carcinoma (RCC) pathogenesis remains unknown. We studied the alterations and functions of SOX7 in RCC. We detected its broad expression in multiple human normal tissues, including kidney, but frequent down‐regulation in RCC cell lines and primary tumors. Promoter CpG methylation seems to directly mediate SOX7 silencing in RCC cells, which could be reversed by demethylation treatment. SOX7 methylation was detected in primary RCC tumors, but rarely in normal kidney tissues. Restoration of SOX7 in silenced 786‐O and A498 RCC cell lines inhibited their cell growth by inducing G0/G1 arrest, whereas SOX7 knockdown promoted RCC cell proliferation. We also found that SOX7 silencing resulted in the activation of WNT signaling and the induction of epithelial to mesenchymal transition. In conclusion, the current study demonstrates that SOX7 is frequently inactivated by promoter CpG methylation in RCC and functions as a tumor suppressor by regulating WNT signaling.—Wang, L., Fan, Y., Zhang, L., Li, L., Kuang, G., Luo, C., Li, C., Xiang, T., Tao, Q., Zhang, Q., Ying, J. Classic SRY‐box protein SOX7 functions as a tumor suppressor regulating WNT signaling and is methylated in renal cell carcinoma. FASEB J. 33, 254–263 (2019). www.fasebj.org
Prevention of Nosocomial Infections in Critically Ill Patients With Lactoferrin: A Randomized, Double-Blind, Placebo-Controlled Study
Authors: Muscedere John , Maslove David M. , Boyd J. Gordon , O’Callaghan Nicole , Sibley Stephanie , Reynolds Steven , Albert Martin , Hall Richard , Jiang Xuran , Day Andrew G. , Jones Gwyneth , Lamontagne Francois 
Published: June 2018

Objective:
To obtain preliminary evidence for the efficacy of lactoferrin as a preventative measure for nosocomial infections and inform the conduct of a definitive study.

Design:
Phase 2, multicenter, randomized, double-blind, placebo-controlled study.

Setting:
Medical-surgical ICUs.

Patients:
Adult, critically ill patients receiving invasive mechanical ventilation.

Interventions:
Randomized, eligible, consenting patients expected to require invasive mechanical ventilation more than 48 hours received lactoferrin both enterally and via an oral swab or a placebo of sterile water for up to 28 days.

Measurements and Main Results:
Of the 214 patients who were randomized, 212 received at least one dose of the intervention and were analyzed (107 lactoferrin and 105 placebo). Protocol adherence was 87.5%. Patients receiving lactoferrin were older (mean [sd], 66.3 [13.5] vs 62.5 [16.2] yr), had a higher Acute Physiology and Chronic Health Evaluation II score (26.8 [7.8] vs 23.5 [7.9]), and need for vasopressors (79% vs 70%). Antibiotic-free days (17.3 [9.0] vs 18.5 [7.1]; p = 0.91) and nosocomial infections (0.3 [0.7] vs 0.4 [0.6] per patient; p = 0.48) did not differ between lactoferrin and placebo groups, respectively. Clinical outcomes for lactoferrin versus placebo were as follows: ICU length of stay (14.5 [18.0] vs 15.0 [37.3] d; p = 0.82), hospital length of stay (25.0 [25.9] vs 28.1 [44.6] d; p = 0.57), hospital mortality (41.1% vs 30.5%; p = 0.11), and 90-day mortality (44.9% vs 32.4%; p = 0.06). Biomarker levels did not differ between the groups.

Conclusions:
Lactoferrin did not improve the primary outcome of antibiotic-free days, nor any of the secondary outcomes. Our data do not support the conduct of a larger phase 3 trial.