bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Contractarian Account of the Crime of Aggression
Authors: Benbaji Yitzhak , Statman Daniel 
Published: November 2019

Abstract
The purpose of this chapter is to explain the moral standing of jus ad bellum as it is formulated in the UN Charter. According to the contract that the Charter embeds, any armed violation of a state’s territorial integrity by another state is an instance of prohibited aggression. As we read it, the Charter confers a moral right against aggression even on states whose borders are unjustly drawn, and even on dangerous states whose political society is irrecoverably divided. In return, states gain a right to go to wars whose aim is to defend their territorial integrity even when such wars are pre-contractually unjust.
The Aims of Just Wars and Jus Ex Bello
Authors: Benbaji Yitzhak , Statman Daniel 
Published: November 2019

Abstract
The chapter discusses the just aims of defensive wars, and, by implication, the duty to end wars, viz., the jus ex bello. It starts with a discussion of the idea of ‘uncompromising wars’ according to which wars may go on until one’s enemy military forces is completely destroyed. We offer a contractarian argument for a rule that categorically prohibits such wars. We then develop two asymmetries between the justice of resort to war and the justice of continuing it. In particular, we show that the conditions of proportionality and of probability of success function differently in constraining resort to war and in constraining its continuation.
The Emotional Crisis of Registration
Authors: Park Yoosun 
Published: November 2019

Abstract
Among the sea of institutionally created troubles that befell Nikkei families in incarceration, arguably the most catastrophic was the family conflict and separation generated by the “loyalty questionnaire,” an administrative debacle which churned violently through the ten camps, splitting apart families and communities for generations to come. Like so many programs of the War Relocation Authority, registration was hastily conceived, inadequately planned, and poorly executed. The fear that they would be forced out of the camps empty-handed into resettlement in unknown and likely hostile locales was a primary reason for many choosing segregation, a choice that should be understood not so much as the Nikkei’s rejection of the United States as the Nikkei’s appraisal of their rejection by the United States. Social workers were involved in all aspects of the registration and the subsequent segregation program, responsible for interviewing all those who opted for segregation and organizing their transfer.
Sensitization of small‐diameter sensory neurons is controlled by TRPV1 and TRPA1 association
Authors: Patil Mayur J. , Salas Margaux , Bialuhin Siarhei , Boyd Jacob T. , Jeske Nathaniel A. , Akopian Armen N. 
Published: November 2019

AbstractUnique features of sensory neuron subtypes are manifest by their distinct physiological and pathophysiological functions. Using patch‐clamp electrophysiology, Ca2+ imaging, calcitonin gene‐related peptide release assay from tissues, protein biochemistry approaches, and behavioral physiology on pain models, this study demonstrates the diversity of sensory neuron pathophysiology is due in part to subtype‐dependent sensitization of TRPV1 and TRPA1. Differential sensitization is influenced by distinct expression of inflammatory mediators, such as prostaglandin E2 (PGE2), bradykinin (BK), and nerve growth factor (NGF) as well as multiple kinases, including protein kinase A (PKA) and C (PKC). However, the co‐expression and interaction of TRPA1 with TRPV1 proved to be the most critical for differential sensitization of sensory neurons. We identified N‐ and C‐terminal domains on TRPV1 responsible for TRPA1‐TRPV1 (A1‐V1) complex formation. Ablation of A1‐V1 complex with dominant‐negative peptides against these domains substantially reduced the sensitization of TRPA1, as well as BK‐ and CFA‐induced hypersensitivity. These data indicate that often occurring TRP channel complexes regulate diversity in neuronal sensitization and may provide a therapeutic target for many neuroinflammatory pain conditions.
Disrupted serial dependence suggests deficits in synaptic potentiation in anti-NMDAR encephalitis and schizophrenia
Authors: Stein H. , Barbosa J. , Rosa-Justicia M. , Prades L. , Morató A. , Galan A. , Ariño H. , Martinez-Hernandez E. , Castro-Fornieles J. , Dalmau J. , Compte A. 
Published: November 2019

AbstractWe report markedly reduced working memory-related serial dependence with preserved memory accuracy in anti-NMDAR encephalitis and schizophrenia. We argue that NMDAR-related changes in cortical excitation, while quickly destabilizing persistent neural activity, cannot fully account for a reduction of memory-dependent biases. Rather, our modeling results support a disruption of a memory mechanism operating on a longer timescale, such as short-term potentiation.
Network analysis reveals a distinct axis of macrophage activation in response to conflicting inflammatory cues
Authors: Liu Xiaji , Zhang Jingyuan , Zeigler Angela C. , Nelson Anders R. , Lindsey Merry L. , Saucerman Jeffrey J. 
Published: November 2019

AbstractMacrophages are subject to a wide range of cytokine and pathogen signals in vivo, which contribute to differential activation and modulation of inflammation. Understanding the response to multiple, often conflicting, cues that macrophages experience requires a network perspective. Here, we integrate data from literature curation and mRNA expression profiles to develop a large-scale computational model of the macrophage signaling network. In response to stimulation across all pairs of 9 cytokine inputs, the model predicted activation along the classic M1-M2 polarization axis but also a second axis of macrophage activation that distinguishes unstimulated macrophages from a mixed phenotype induced by conflicting cues. Along this second axis, combinations of conflicting stimuli, interleukin 4 (IL4) with lipopolysaccharide (LPS), interferon-γ (IFNγ), IFNβ, or tumor necrosis factor-α (TNFα), produced mutual inhibition of several signaling pathways, e.g. nuclear factor κB (NFκB) and signal transducer and activator of transcription 6 (STAT6), but also mutual activation of the phosphoinositide 3-kinases (PI3K) signaling module. In response to combined IFNγ and IL4, the model predicted genes whose expression was mutually inhibited, e.g. inducible nitric oxide synthase (iNOS) and arginase 1 (Arg1), or mutually enhanced, e.g. IL4 receptor-α (IL4Rα) and suppressor of cytokine signaling 1 (SOCS1), which was validated by independent experimental data. Knockdown simulations further predicted network mechanisms underlying functional crosstalk, such as mutual STAT3/STAT6-mediated enhancement of IL4Rα expression. In summary, the computational model predicts that network crosstalk mediates a broadened spectrum of macrophage activation in response to mixed pro- and anti-inflammatory cytokine cues, making it useful for modeling in vivo scenarios.Summary sentenceNetwork modeling of macrophage activation predicts responses to combinations of cytokines along both the M1-M2 polarization axis and a second axis associated with a mixed macrophage activation phenotype.
Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oysterCrassostrea gigasthroughout the Northern Hemisphere
Authors: Sutherland Ben J. G. , Rycroft Claire , Ferchaud Anne-Laure , Saunders Rob , Li Li , Liu Sheng , Chan Amy M. , Otto Sarah P. , Suttle Curtis A. , Miller Kristina M. 
Published: November 2019

ABSTRACTPacific oysterCrassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self-sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery-farmed) or naturalized/wild oysters to move onto a farm (naturalized-farmed). It is therefore important to understand genetic variation among populations and farm types. Here we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double-digest RAD-sequencing in 182 naturalized, 112 hatchery-farmed, and 72 naturalized-farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST= 0.0019), and low differentiation between countries in the Japan-Canada-France historical translocation lineage (France-Canada FST= 0.0024; Japan-Canada FST= 0.0060). Chinese populations were more differentiated (China-Japan FST= 0.0241). Hatchery-propagated populations had higher inter-individual relatedness suggesting family structure. Within-population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate was lower in one farm population. Moving oysters from nature onto farms did not result in strong within-generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting non-local origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery-farmed oysters depends on whether naturalized populations are valued as a locally-adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.
The origin and spread of locally adaptive seasonal camouflage in snowshoe hares
Authors: Jones Matthew R. , Mills L. Scott , Jensen Jeffrey D. , Good Jeffrey M. 
Published: November 2019

AbstractAdaptation is central to population persistence in the face of environmental change, yet we rarely precisely understand the origin and spread of adaptive variation in natural populations. Snowshoe hares (Lepus americanus) along the Pacific Northwest (PNW) coast have evolved brown winter camouflage through positive selection on recessive variation at theAgoutipigmentation gene introgressed from black-tailed jackrabbits (L. californicus). Here we combine new and published whole genome and exome sequences with targeted genotyping ofAgoutiin order to investigate the evolutionary history of local seasonal camouflage adaptation in the PNW. We find evidence of significantly elevated inbreeding and mutational load in coastal winter-brown hares, consistent with a recent range expansion into temperate coastal environments that incurred indirect fitness costs. The genome-wide distribution of introgression tract lengths supports a pulse of hybridization near the end of the last glacial maximum, which may have facilitated range expansion via introgression of winter-brown camouflage variation. However, signatures of a selective sweep atAgoutiindicate a much more recent spread of winter-brown camouflage. Through simulations we show that the temporal lag between the hybrid origin and subsequent selective sweep of the recessive winter-brown allele can be largely attributed to the limits of natural selection imposed by simple allelic dominance. We argue that while hybridization during periods of environmental change may provide a critical reservoir of adaptive variation at range edges, the probability and pace of local adaptation will strongly depend on population demography and the genetic architecture of introgressed variation.
Modeling motor-evoked potentials from neural field simulations of transcranial magnetic stimulation
Authors: Wilson Marcus T , Moezzi Bahar , Rogasch Nigel C 
Published: November 2019

AbstractObjectiveTo develop a population-based biophysical model of motor-evoked potentials (MEPs) following transcranial magnetic stimulation (TMS).MethodsWe combined an existing MEP model with population-based cortical modeling. Layer 2/3 excitatory and inhibitory neural populations, modeled with neural-field theory, are stimulated with TMS and feed layer 5 corticospinal neurons, which also couple directly but weakly to the TMS pulse. The layer 5 output controls mean motoneuron responses, which generate a series of single motor-unit action potentials that are summed to estimate a MEP.ResultsA MEP waveform was generated comparable to those observed experimentally. The model captured TMS phenomena including a sigmoidal input-output curve, common paired pulse effects (short interval intracortical inhibition, intracortical facilitation, long interval intracortical inhibition) including responses to pharmacological interventions, and a cortical silent period. Changes in MEP amplitude following theta burst paradigms were observed including variability in outcome direction.ConclusionsThe model reproduces effects seen in common TMS paradigms.SignificanceThe model allows population-based modeling of changes in cortical dynamics due to TMS protocols to be assessed in terms of changes in MEPs, thus allowing a clear comparison between population-based modeling predictions and typical experimental outcome measures.HighlightsA model of motor-evoked potential formation gives a realistic electromyogram in response to TMS.The model reproduces effects of SICI, ICF and LICI.A link between existing neural field modeling and realistic outcome measures of TMS is provided.
Pharmacological complementation remedies an inborn error of lipid metabolism
Authors: Hartley Meredith D. , Shokat Mitra D. , DeBell Margaret J. , Banerji Tania , Kirkemo Lisa L. , Scanlan Thomas S. 
Published: November 2019

SummaryX-linked adrenoleukodystrophy (X-ALD) is a rare, genetic disease in which increased very long chain fatty acids (VLCFAs) in the central nervous system (CNS) cause demyelination and axonal degeneration, leading to severe neurological deficits. Sobetirome, a potent thyroid hormone agonist, has been shown to lower VLCFA levels in the periphery and CNS. In this study, two pharmacological strategies for enhancing the effects of thyromimetics were tested in Abcd1 KO mice, a murine model that has the same inborn error in metabolism as X-ALD patients. First, a sobetirome prodrug (Sob-AM2) with increased CNS penetration lowered CNS VLCFAs more potently than sobetirome, and was better tolerated with lower peripheral exposure, but was unable to unable to break the efficacy threshold of CNS VLCFA lowering in Abcd1 KO mice. Second, co-administration of thyroid hormone with sobetirome enhanced VLCFA lowering in the periphery compared to sobetirome alone but did not produce greater lowering in the CNS. These data suggest that the extent of CNS VLCFA lowering in Abcd1 KO mice is limited by a mechanistic threshold related to slow turnover kinetics, potentially related to the lack of frank X-ALD disease in this model. However, Sob-AM2 has improved potency at correcting the lipid abnormality associated with X-ALD in the CNS with better tolerance than the parent drug sobetirome.
Automated cot-side tracking of functional brain age in preterm infants
Authors: Stevenson Nathan J. , Oberdorfer Lisa , Tataranno Maria-Luisa , Breakspear Michael , Colditz Paul B. , de Vries Linda S. , Benders Manon J. N. L. , Klebermass-Schrehof Katrin , Vanhatalo Sampsa , Roberts James A. 
Published: November 2019

AbstractObjectiveA major challenge in the care of preterm infants is the early identification of compromised neurological development. While several measures are routinely used to track anatomical growth, there is a striking lack of reliable and objective tools for tracking maturation of early brain function; a cornerstone of lifelong neurological health. We present a cot-side method for measuring the functional maturity of the newborn brain based on routinely-available neurological monitoring with electroencephalography (EEG).MethodsWe used a dataset of 177 EEG recordings from 65 preterm infants to train a multivariable prediction of functional brain age (FBA) from EEG. The FBA was validated on an independent set of 99 EEG recordings from 42 preterm infants. The difference between FBA and postmenstrual age (PMA) was evaluated as a predictor for neurodevelopmental outcome.ResultsThe FBA correlated strongly with the PMA of an infant, with a median prediction error of less than 1 week. Moreover, individual babies follow well-defined individual trajectories. The accuracy of the FBA applied to the validation set was statistically equivalent to the training set accuracy. In a subgroup of infants with repeated EEG recordings, a persistently negative predicted age difference was associated with poor neurodevelopmental outcome.InterpretationThe FBA enables the tracking of functional neurodevelopment in preterm infants. This establishes proof of principle for growth charts for brain function, a new tool to assist clinical management and identify infants who will benefit most from early intervention.
Fungal communities (Mycobiome) as potential ecological indicators within confluence stretch of Ganges and Yamuna Rivers, India
Authors: Samson Rachel , Rajput Vinay , Shah Manan , Yadav Rakeshkumar , Sarode Priyanka , Dastager Syed G. , Dharne Mahesh S. , Khairnar Krishna 
Published: November 2019

AbstractRiver confluences are a hub of biodiversity with limited information with respect to the structure and the functions of the microbial communities. The ‘River Ganges’ is the national river of India, having manifold significance such as social, mythological, historic, geographic and agro-economic. It forms a sacred confluence (known asTriveni Sangam) with River Yamuna at Prayagraj, India. Recent reports indicated the presence of fecal coliform bacteria, an indicator recognized for water contamination in Ganges River leading to pollution. However, Fungi are also gaining attention as potential biological indicators of the trophic status of some rivers globally, but remain under-explored in terms of diversity, ecology and functional aspects. We performed whole long read, metagenome sequencing (MinION) of the sediment samples collected in December 2017 from confluence zone of Ganges and Yamuna Rivers spanning the pre-confluence, confluence and post-confluence zones. Mycobiome reads revealed a plethora of fungal communities, extending from saprophytes, endoparasites and edible fungi, to human pathogens, plant pathogens and toxin producers. The fungal genera recognized as bio-indicators of river pollution (Aspergillus,Penicillium) and eutrophication (Kluveromyces,Lodderomyces, andNakaseomyces), were present in all samples. Functional gene analyses of myco-communities uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bio-indicators of pollution. This study forms a foundational basis for understanding the impact of various anthropogenic activities on the mycobiome, as a bio-indicator of pollution across the confluence of Ganges and Yamuna Rivers and post-confluence of River Ganges, and could be useful in mitigating strategies for cleaning strategies of the Ganges River.
Disentangling functional connectivity effects of age and expertise in long-term meditators
Authors: Guidotti Roberto , Gratta Cosimo Del , Perrucci Mauro Gianni , Romani Gian Luca , Raffone Antonino 
Published: November 2019

AbstractThe effects of intensive meditation practices on the functional and structural organization of the human brain have been addressed by a growing number of neuroscientific studies. However, the different modulations of meditation expertise and of ageing, in the underlying brain areas and networks, have not yet been fully elucidated. These effects should be distinguished in order to clarify how long-term meditation can modulate the connectivity between brain areas. To address this issue, we tested whether meditation expertise and age can be predicted from the multivariate pattern of functional Magnetic Resonance Imaging connectivity, in Theravada Buddhist monks with long-term practice in two different meditation forms: Focused Attention (FA) and Open Monitoring (OM).We found that functional connectivity patterns in both meditation forms can be used to predict expertise and age of long-term meditators. Our findings suggest that meditation expertise is associated with meditation-specific brain networks modulations, while age-related modifications are general and independent from the meditation type. Specifically, expertise modulated patterns during FA meditation include nodes and connections implicated in focusing, sustaining and monitoring attention, while the predictive patterns during OM meditation include nodes associated with cognitive and affective monitoring. Thus, the two forms of meditation may differentially contribute to counteract the effects of neurocognitive decline with ageing by neuroplasticity of brain networks.
Large male proboscis monkeys have larger noses but smaller canines
Authors: Matsuda Ikki , Stark Danica J. , Ramirez Saldivar Diana A. , Tuuga Augustine , Nathan Senthilvel K. S. S. , Goossens Benoit , van Schaik Carel P. , Koda Hiroki 
Published: November 2019

AbstractThe uniquely enlarged noses of male proboscis monkeys are prominent adornments, and a sexually selected male trait. A recent study showed significant correlations among nose, body, and testis sizes and clear associations between nose size and the number of females in a male’s harem. However, to date, the analyses of other common male traits, i.e., canines, are lacking. Whereas male nose size had a positive correlation with body size, we unexpectedly found a negative correlation between body and canine sizes. We explain this by an interaction between sexual and natural selection. Larger noses in males may interfere with the use of canines, thereby reducing their effectiveness as weapons. Additionally, longer canines are opposed by natural selection because the larger gape it imposes upon its bearer reduces foraging efficiency, particularly in folivores. This unique case of decoupling of body and canine size reveals that large canines carry an ecological cost.
Statistical inference of mechanistic models from qualitative data using an efficient optimal scaling approach
Authors: Schmiester Leonard , Weindl Daniel , Hasenauer Jan 
Published: November 2019

AbstractQuantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. These models usually comprise unknown parameters, which have to be inferred from experimental data. For quantitative experimental data, there are several methods and software tools available. However, for qualitative data the available approaches are limited and computationally demanding.Here, we consider the optimal scaling method which has been developed in statistics for categorical data and has been applied to dynamical systems. This approach turns qualitative variables into quantitative ones, accounting for constraints on their relation. We derive a reduced formulation for the optimization problem defining the optimal scaling. The reduced formulation possesses the same optimal points as the established formulation but requires less degrees of freedom. Parameter estimation for dynamical models of cellular pathways revealed that the reduced formulation improves the robustness and convergence of optimizers. This resulted in substantially reduced computation times.We implemented the proposed approach in the open-source Python Parameter EStimation TOolbox (pyPESTO) to facilitate reuse and extension. The proposed approach enables efficient parameterization of quantitative dynamical models using qualitative data.