bluuebunny/crossref_metadata_2025_split huggingface dataset:
Agreement mismatches in Dutch relatives
Authors: Bouma Gosse 
Published: April 2018

AbstractThis paper investigates agreement mismatches in Dutch relatives. While the norm is that singular neuter nouns occur with the relative pronoundat‘that’, it is by now quite common to find neuter nouns combining with the relative pronoundie. A large Twitter corpus is used to study which linguistic variables makedie‘that’ in this context more likely. Lack of agreement between neuter noun and relative pronoun is very frequent in this corpus (37.5% of the cases, 46.8% if the preceding determiner is indefinite). Non-agreement is most common for nouns that are high in the animacy ranking, but it also occurs with other semantic classes, and there is quite a bit of lexical variation. Young, female users have a stronger tendency to use non-agreeing relative pronouns. Contrary to what previous work suggests, we do not find that users with a Moroccan or Turkish background have a stronger tendency towards non-agreement. A comparison of tweets with agreeing and non-agreeing pronouns and a comparison of the Twitter corpus with web data both suggest that non-agreement is characteristic of informal language use.
Scales or features in verb meaning?
Authors: Verhoeven Elisabeth 
Published: April 2018

AbstractSeveral syntactic properties of verbal heads are accounted for through their semantic properties. Verbal features such as agentivity, volitionality, stativity etc. have been proven a useful tool for predicting several aspects of their syntactic behavior such as passivization, auxiliary selection etc. In the context of the empirical turn in current linguistics, the assumption of discrete features is questioned by studies based on corpora or speakers’ intuitions showing that the diagnostics of semantic features involve gradience. These findings are challenging for grammatical theory: are we justified to assume the existence of discrete verb classes or do the established properties indicate scalar dimensions of meaning? Based on two empirical studies – an acceptability study and a corpus study – the present article examines the role ofagentivityin distinguishing verb classes and in predicting the syntactic behavior of verbs in German. Acceptability data show that the diagnostics of agentivity involve gradience, which cannot be reduced to random sources of variation. However, a comparison of scalar vs. categorical models of agentivity based on these diagnostics reveals that the syntactic variation in word order found in written corpus data is best accounted for through a model that assumes a binary division into a ±agentive and a non-agentive verb class.
Accounting for syntactic variation in diachrony
Authors: Granvik Anton 
Published: April 2018

AbstractThis paper addresses the early variation in what has been called the [prep_que] variable in Spanish nominal complement clauses, i.e. the alternation betweende queandquein examples such asenseñal (de) quelo estimo, Zulema, este anillo ofrezco(CORDE) ‘as a sign that I appreciate You, Zulema, I offer this ring’. By applying several subsequent quantitative analyses on corpus instances of the sequences Nde queand Nque, the locus of variation is restricted to such an extent that the variation can largely be accounted for. A collostructional analysis identifies 31 central nouns of the Nde quecomplement clause construction. A diachronic cluster analysis delimits the temporal dimension of the variation to the 16th and 17th centuries. A distinctive collexeme analysis identifies nine nouns which are used in both constructional formats to a comparable degree:causa‘cause’,duda‘doubt’,esperanza‘hope’,fe‘faith’,opinión‘opinion’,recelo‘fear’,señal‘sign(al)’,sospecha‘suspicion’, andtemor‘fear’. Detailed contextual analysis of the use of these nine nouns by means of a mixed-effects logistic regression reveals that the use of the nouns with a determiner is correlated with thede quevariant, and the use of the nouns as part of complex predicates, as intener sospecha‘have suspicion’, is associated with thequevariant of the complement clause.
A Century of U.S. Farm Productivity Growth: A Surge Then a Slowdown
Authors: Andersen Matthew A , Alston Julian M , Pardey Philip G , Smith Aaron 
Published: April 2018

AbstractU.S. farm productivity growth has direct consequences for sustainably feeding the world's still rapidly growing population, as well as U.S. competitiveness in international markets. Using a newly expanded compilation of multifactor productivity (MFP) estimates and associated partial‐factor productivity (PFP) measures, we examine changes in the pattern of U.S. agricultural productivity growth over the past century and more. Considering the evidence as a whole, we detect sizable and significant slowdowns in the rate of productivity growth in recent decades. U.S. multifactor productivity grew at an annual average rate of just 1.16% per year during 1990–2007 compared with 1.42% per year for the period 1910–2007. U.S. yields of major crops grew at an annual average rate of 1.17% per year for 1990–2009 compared with 1.81% per year for 1936–1990. More subtly, but with potentially profound implications, the relatively high rates of MFP growth during the third quarter of the century are an historical aberration relative to the long‐run trend.
PathwaySplice: an R package for unbiased pathway analysis of alternative splicing in RNA-Seq data
Authors: Yan Aimin , Ban Yuguang , Gao Zhen , Chen Xi , Wang Lily 
Published: April 2018

AbstractSummaryPathway analysis of alternative splicing would be biased without accounting for the different number of exons or junctions associated with each gene, because genes with higher number of exons or junctions are more likely to be included in the ‘significant’ gene list in alternative splicing. We present PathwaySplice, an R package that (i) Performs pathway analysis that explicitly adjusts for the number of exons or junctions associated with each gene; (ii) visualizes selection bias due to different number of exons or junctions for each gene and formally tests for presence of bias using logistic regression; (iii) supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets; (iv) identifies the significant genes driving pathway significance and (v) organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph.Availability and implementationhttps://bioconductor.org/packages/release/bioc/html/PathwaySplice.htmlSupplementary informationSupplementary data are available at Bioinformatics online.
Large-scale Artemisinin–Piperaquine Mass Drug Administration With or Without Primaquine Dramatically Reduces Malaria in a Highly Endemic Region of Africa
Authors: Deng Changsheng , Huang Bo , Wang Qi , Wu Wanting , Zheng Shaoqin , Zhang Hongying , Li Di , Feng Danghong , Li Guoming , Xue Linlu , Yang Tao , Tuo Fei , Mohadji Fouad , Su Xin-zhuan , Xu Qin , Wu Zhibing , Lin Li , Zhou Jiuyao , Yan Hong , Bacar Affane , Said Abdallah Kamal , Kéké Rachadi A , Msa Mliva Ahamada , Mohamed Moussa , Wang Xinhua , Huang Shiguang , Oithik Fatihou , Li Xiao-bo , Lu Fangli , Fay Michael P , Liu Xiao-hong , Wellems Thomas E , Song Jianping 
Published: April 2018

Abstract

Background
Mass drug administration (MDA), with or without low-dose primaquine (PMQLD), is being considered for malaria elimination programs. The potential of PMQLD to block malaria transmission by mosquitoes must be balanced against liabilities of its use.

Methods
Artemisinin–piperaquine (AP), with or without PMQLD, was administered in 3 monthly rounds across Anjouan Island, Union of Comoros. Plasmodium falciparum malaria rates, mortality, parasitemias, adverse events, and PfK13 Kelch-propeller gene polymorphisms were evaluated.

Results
Coverage of 85 to 93% of the Anjouan population was achieved with AP plus PMQLD (AP+PMQLD) in 2 districts (population 97164) and with AP alone in 5 districts (224471). Between the months of April–September in both 2012 and 2013, average monthly malaria hospital rates per 100000 people fell from 310.8 to 2.06 in the AP+PMQLD population (ratio 2.06/310.8 = 0.66%; 95% CI: 0.02%, 3.62%; P = .00007) and from 412.1 to 2.60 in the AP population (ratio 0.63%; 95% CI: 0.11%, 1.93%; P &lt; .00001). Effectiveness of AP+PMQLD was 0.9908 (95% CI: 0.9053, 0.9991), while effectiveness of AP alone was 0.9913 (95% CI: 0.9657, 0.9978). Both regimens were well tolerated, without severe adverse events. Analysis of 52 malaria samples after MDA showed no evidence for selection of PfK13 Kelch-propeller mutations.

Conclusions
Steep reductions of malaria cases were achieved by 3 monthly rounds of either AP+PMQLD or AP alone, suggesting potential for highly successful MDA without PMQLD in epidemiological settings such as those on Anjouan. A major challenge is to sustain and expand the public health benefits of malaria reductions by MDA.
Methotrexate for the Treatment of Pediatric Crohn’s Disease: A Systematic Review and Meta-analysis
Authors: Colman Ruben J , Lawton Rachel C , Dubinsky Marla C , Rubin David T 
Published: April 2018

Abstract

Background
Methotrexate (MTX) is an immunomodulator used for the treatment of pediatric inflammatory bowel disease (IBD). There are currently no RCTs that assess the treatment efficacy of methotrexate within the pediatric IBD patient population. This systematic review and meta-analysis assesses the efficacy of MTX therapy among the existing pediatric literature.

Methods
A systematic literature search was performed using MEDLINE and the Cochrane library from inception until March 2016. Synonyms for ‘pediatric’, ‘methotrexate’ and ‘IBD’ were utilized as both free text and MESH search terms. The studies included contained clinical remission (CR) rates for MTX treatment of pediatric IBD patients 18 yrs old, as mono- or combination therapy. Case studies with <10 patients were excluded. Quality assessment was performed with the Newcastle-Ottawa Scale. Meta-analysis calculated pooled CR rates. A random-effects meta-analysis with forest plots was performed using R.

Results
Fourteen (11 monotherapy, 1 combination therapy, 2 both; n = 886 patients) observational studies were eligible out of 202 studies. No interventional studies were identified. The pooled achieved CR rate for pediatric CD patients on monotherapy within 3-6 months was 57.7% (95% CI 48.2-66.6%), (P =0.22; I2 = 29.8%). The CR was 37.1% (95% CI 29.5-45.5%), (P = 0.20; I2 = 37.4%) for maintenance therapy at 12 months. Sub-analysis could not identify CR differences between MTX administration types, thiopurine exposure.

Conclusions
This meta-analysis demonstrated that, over 50% of pediatric Crohn’s disease patients induced with methotrexate achieved clinical remission, while 12-month remission rate was only 37%. Prospective controlled interventional trials should assess treatment efficacy among patient subgroups.
Stratification for Multiplicative Character Sums
Authors: Xu Junyan 
Published: April 2018

AbstractWe prove a stratification result for certain families of n-dimensional (complete algebraic) multiplicative character sums. The character sums we consider are sums of products of r multiplicative characters evaluated at rational functions, and the families (with nr parameters) are obtained by allowing each of the r rational functions to be replaced by an “offset”, that is, a translate, of itself. For very general such families, we show that the stratum of the parameter space on which the character sum has maximum weight $n+j$ has codimension at least j⌊(r − 1)/2(n − 1)⌋ for 1 ≤ j ≤ n − 1 and ⌈nr/2⌉ for j = n. This result is used to obtain multivariate Burgess bounds in joint work with Lillian Pierce.
The ‘Abe Doctrine’: Japan’s new regional realism
Authors: Envall H D P 
Published: April 2018

AbstractSince 2012, Japan’s Prime Minister Abe Shinzō has sought to remake the country’s foreign and security policy. Abe’s agenda, which is increasingly called an ‘Abe Doctrine’, has prompted considerable debate as to its true nature. Is the Abe Doctrine nationalist, revisionist, or realist? This article contributes to these debates by tracing the competing characterizations of an Abe Doctrine’s policy ideas and assessing these against the doctrine’s policy prescriptions. It argues that the Abe Doctrine–situated within the long-term evolution of Japanese policymaking – is chiefly realist rather than nationalist in its policy prescriptions. In fact, where the doctrine does constitute a major departure from past policy practice, largely unrecognized until now, is not so much in how it expands Japan’s international role but in how it narrows this role. The underlying logic of the Abe Doctrine may therefore be pushing Japan towards a new form of regional realism.
The pulsationally modulated radial crossover signature of the slowly rotating magnetic B-type star ξ1 CMa
Authors: Shultz M , Kochukhov O , Wade G A , Rivinius Th 
Published: April 2018

Abstract
We report the latest set of spectropolarimetric observations of the magnetic β Cep star ξ1 CMa. The new observations confirm the long-period model of Shultz et al. (2017), who proposed a rotational period of about 30 years and predicted that in 2018 the star should pass through a magnetic null. In perfect agreement with this projection, all longitudinal magnetic field ⟨Bz⟩ measurements are close to 0 G. Remarkably, individual Stokes V profiles all display a crossover signature, which is consistent with ⟨Bz⟩ ∼ 0 but is not expected when v sin i ∼ 0. The crossover signatures furthermore exhibit pulsationally modulated amplitude and sign variations. We show that these unexpected phenomena can all be explained by a ‘radial crossover’ effect related to the star’s radial pulsations, together with an important deviation of the global field topology from a purely dipolar structure, that we explore via a dipole+quadrupole configuration as the simplest non-dipolar field.
Risk factors for death in kidney transplant patients: analysis from a large protocol biopsy registry
Authors: Abeling Tanja , Scheffner Irina , Karch Annika , Broecker Verena , Koch Armin , Haller Hermann , Schwarz Anke , Gwinner Wilfried 
Published: April 2018

Abstract

Background
Identification and quantification of the relevant factors for death can improve patients’ individual risk assessment and decision-making. We used a well-documented patient cohort (n = 892) in a renal transplant programme with protocol biopsies to establish multivariable Cox models for risk assessment at 3 and 12 months post-transplantation.

Methods
Patients transplanted between 2000 and 2007 were observed up to 11 years (total observation 5227 patient-years; median 5.9 years). Loss to follow-up was negligible (n = 15). A total of 2251 protocol biopsies and 1214 biopsies for cause were performed. All rejections and clinical borderline rejections in protocol biopsies were treated.

Results
Overall 10-year patient survival was 78%, with inferior survival of patients with graft loss and superior survival of patients with living-donor transplantation. Eight factors were common in the models at 3 and 12 months, including age, pre-transplant heart failure and a score of cardiovascular disease and type 2 diabetes, post-transplant urinary tract infection, treatment of rejection, new-onset heart failure, coronary events and malignancies. Additional variables of the model at 3 months included deceased donor transplantation, transplant lymphocele, BK virus nephropathy and severe infections. Graft function and graft loss were significant factors of the model at 12 months. Internal validation and validation with a separate cohort of patients (n = 349) demonstrated good discrimination of the models.

Conclusions
The identified factors indicate the important areas that need special attention in the pre- and post-transplant care of renal transplant patients. On the basis of these models, we provide nomograms as a tool to weigh individual risks that may contribute to decreased survival.
Emergence of Resistance to Colistin During the Treatment of Bloodstream Infection Caused by Klebsiella pneumoniae Carbapenemase–Producing Klebsiella pneumoniae
Authors: Kanwar Anubhav , Marshall Steven H , Perez Federico , Tomas Myreen , Jacobs Michael R , Hujer Andrea M , Domitrovic T Nicholas , Rudin Susan D , Rojas Laura J , Kreiswirth Barry N , Chen Liang , Quinones-Mateu Miguel , van Duin David , Bonomo Robert A ,   Antibacterial Resistance Leadership Group
Published: April 2018

Abstract
We report the emergence of colistin resistance in Klebsiella pneumoniae carbapenemase (KPC)–producing Klebsiella pneumoniae after 8 days of colistin-based therapy, resulting in relapse of bloodstream infection and death. Disruption of the mgrB gene by insertion of a mobile genetic element was found to be the mechanism, which was replicated in vitro after exposure to subinhibitory concentrations of colistin and meropenem.
Over a thousand new periodic orbits of a planar three-body system with unequal masses
Authors: Li Xiaoming , Jing Yipeng , Liao Shijun 
Published: April 2018

Abstract
The three-body problem is common in astronomy, examples of which are the solar system, exoplanets, and stellar systems. Due to its chaotic characteristic, discovered by Poincaré, only three families of periodic three-body orbits were found in 300 years, until 2013 when Šuvakov and Dmitrašinović (2013, Phys. Rev. Lett., 110, 114301) found 13 new periodic orbits of a Newtonian planar three-body problem with equal mass. Recently, more than 600 new families of periodic orbits of triple systems with equal mass were found by Li and Liao (2017, Sci. China-Phys. Mech. Astron., 60, 129511). Here, we report 1349 new families of planar periodic orbits of the triple system where two bodies have the same mass and the other has a different mass. None of the families have ever been reported, except the famous “figure-eight” family. In particular, 1223 among these 1349 families are entirely new, i.e., with newly found “free group elements” that have been never reported, even for three-body systems with equal mass. It has been traditionally believed that triple systems are often unstable if they are non-hierarchical. However, all of our new periodic orbits are in non-hierarchical configurations, but many of them are either linearly or marginally stable. This might inspire the long-term astronomical observation of stable non-hierarchical triple systems in practice. In addition, using these new periodic orbits as initial guesses, new periodic orbits of triple systems with three unequal masses can be found by means of the continuation method, which is more general and thus should have practical meaning from an astronomical viewpoint.
Impact of dietary gut microbial metabolites on the epigenome
Authors: Gerhauser Clarissa 
Published: April 2018

Within the past decade, epigenetic mechanisms and their modulation by natural products have gained increasing interest. Dietary bioactive compounds from various sources, including green tea, soya, fruit and berries, cruciferous vegetables, whole grain foods, fish and others, have been shown to target enzymes involved in epigenetic gene regulation, including DNA methyltransferases, histone acetyltransferases, deacetylases and demethylasesin vitroand in cell culture. Also, many dietary agents were shown to alter miRNA expression.In vivostudies in animal models and humans are still limited. Recent research has indicated that the gut microbiota and gut microbial metabolites might be important mediators of diet–epigenome interactions. Inter-individual differences in the gut microbiome might affect release, metabolism and bioavailability of dietary agents and explain variability in response to intervention in human studies. Only a few microbial metabolites, including folate, phenolic acids,S-(−)equol, urolithins, isothiocyanates, and short- and long-chain fatty acids have been tested with respect to their potential to influence epigenetic mechanisms. Considering that a complex mixture of intermediary and microbial metabolites is present in human circulation, a more systematic interdisciplinary investigation of nutri-epigenetic activities and their impact on human health is called for.This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.
CD117/c-kit Defines a Prostate CSC-Like Subpopulation Driving Progression and TKI Resistance
Authors: Harris Koran S. , Shi Lihong , Foster Brittni M. , Mobley Mary E. , Elliott Phyllis L. , Song Conner J. , Watabe Kounosuke , Langefeld Carl D. , Kerr Bethany A. 
Published: April 2018

ABSTRACTCancer stem-like cells (CSCs) are associated with cancer progression, metastasis, and recurrence, and may also represent a subset of circulating tumor cells (CTCs). In our prior study, CTCs in advanced prostate cancer patients were found to express CD117/c-kit in a liquid biopsy. Whether CD117 expression played an active or passive role in the aggressiveness and migration of these CTCs remained an open question. In this study, we show that CD117 expression in prostate cancer patients is associated with decreased overall and progression-free survival and that activation and phosphorylation of CD117 increases in prostate cancer patients with higher Gleason grades. To determine how CD117 expression and activation by its ligand stem cell factor (SCF, kit ligand, steel factor) alter prostate cancer aggressiveness, we used LNCaP-C4-2 and PC3-mm human prostate cancer cells, which contain a CD117+ subpopulation. We demonstrate that CD117+ cells display increased proliferation and migration. In prostaspheres, CD117 expression enhances sphere formation. In both 2D and 3D cultures, stemness marker gene expression is higher in CD117+ cells. Using xenograft limiting dilution assays and serial tumor initiation assays, we show that CD117+ cells represent a CSC population. Combined, these data indicate that CD117 expression potentially promotes tumor initiation and metastasis. Further, in cell lines, CD117 activation by SCF promotes faster proliferation and invasiveness, while blocking CD117 activation with tyrosine kinase inhibitors (TKIs) decreased progression in a context-dependent manner. We demonstrate that CD117 expression and activation drives prostate cancer aggressiveness through the CSC phenotype and TKI resistance.
Generalised free energy and active inference: can the future cause the past?
Authors: Parr Thomas , Friston Karl J 
Published: April 2018

AbstractWe compare two free energy functionals for active inference under Markov decision processes. One of these is a functional of beliefs about states and policies, but a function of observations, while the second is a functional of beliefs about all three. In the former (expected free energy), prior beliefs about outcomes are not part of the generative model (because they are absorbed into the prior over policies). Conversely, in the second (generalised free energy); priors over outcomes become an explicit component of the generative model. When using the free energy function, which is blind to counterfactual (i.e., future) observations, we equip the generative model with a prior over policies that ensure preferred (i.e., priors over) outcomes are realised. In other words, selected policies minimise uncertainty about future outcomes by minimising the free energy expected in the future. When using the free energy functional – that effectively treats counterfactual observations as hidden states – we show that policies are inferred or selected that realise prior preferences by minimising the free energy of future expectations. Interestingly, the form of posterior beliefs about policies (and associated belief updating) turns out to be identical under both formulations, but the quantities used to compute them are not.