bluuebunny/crossref_metadata_2025_split huggingface dataset:
Maps of subjective feelings
Authors: Nummenmaa Lauri , Hari Riitta , Hietanen Jari K. , Glerean Enrico 
Published: August 2018

Significance
Subjective feelings are a central feature of human life, yet their relative organization has remained elusive. We mapped the “human feeling space” for 100 core feelings ranging from cognitive and affective processes to somatic sensations; in the analysis, we combined basic dimension rating, similarity mapping, bodily sensation mapping, and neuroimaging meta-analysis. All feelings were emotionally loaded, and saliencies of bodily and mental experiences were correlated. Feelings formed five groups: positive emotions, negative emotions, cognitive processes, somatic states, and homeostatic states. Feeling space was best explained by emotionality, mental experience, and bodily sensation topographies. Subjectively felt similarity of feelings was associated with basic feeling dimensions and the bodily sensation maps. This shows that subjective feelings are categorical, emotional, and embodied.
Mechanics of elastomeric molecular composites
Authors: Millereau Pierre , Ducrot Etienne , Clough Jess M. , Wiseman Meredith E. , Brown Hugh R. , Sijbesma Rint P. , Creton Costantino 
Published: August 2018

Significance
Soft materials have been made tough by introducing nanofiller particles, which significantly stiffen and toughen the material. Stiffening is understood, but the reason for the toughening is not. We have developed a model system of molecular composites where the filler is a continuous network embedded into a stretchy matrix. By combining design of networks, mechanical testing in the nonlinear regime, and incorporation of mechanophore molecules as cross-linkers, we demonstrate how the composites can stiffen at a desired level of extension; soften by breaking bonds in the stiff filler network; and, for certain compositions, resist crack propagation by transferring stress to the stretchy matrix network. Macroscopic and molecular insight provides a detailed picture of how failure occurs in complex soft materials.
Changes in membrane properties of rat deep cerebellar nuclear projection neurons during acquisition of eyeblink conditioning
Authors: Wang Desheng , Smith-Bell Carrie A. , Burhans Lauren B. , O’Dell Deidre E. , Bell Roger W. , Schreurs Bernard G. 
Published: August 2018

SignificanceAlthough large ensembles of neurons have been found to change as a function of learning and memory, localizing those changes to the individual neurons directly involved in a specific task has been challenging. Using whole-cell recording of deep cerebellar nuclear neurons (DCN) and a transsynaptic viral tracer, we found motor learning induced significant changes in membrane properties of rat DCN projection neurons including a reduced after-hyperpolarization amplitude and shortened latency for both evoked DCN action potentials and rebound spikes. These learning-specific changes in DCN excitability have not previously been reported in any species or task.
Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability
Authors: Moss Frank R. , Shuken Steven R. , Mercer Jaron A. M. , Cohen Carolyn M. , Weiss Thomas M. , Boxer Steven G. , Burns Noah Z. 
Published: August 2018

Significance
Ladderane lipids represent exotic natural products containing highly strained, concatenated cyclobutane rings, a motif that has not been found in any other natural products. These lipids are exclusively found in bacteria that carry out anaerobic ammonium oxidation (anammox), suggesting a biological role in the anammox process. The relationship between molecular structure and this metabolism remains unexplored due to a lack of natural lipid material to study. We use an efficient chemical synthesis to create large quantities of pure ladderane lipids for biophysical analysis. This analysis reveals some unusual properties of membranes composed of ladderane lipids. Significantly, ladderane membranes have low proton permeability, which would slow the breakdown of the proton gradient used to synthesize ATP during the slow anammox metabolism.
Insights into CD47/SIRPα axis-targeting tumor immunotherapy
Authors: Zhang Xuyao , Fan Jiajun , Ju Dianwen 
Published: August 2018

ABSTRACT
During the last decade, inhibitors targeting immune checkpoint programmed death ligand 1/PD-1 and cytotoxic T-lymphocyte-associated protein 4 have been one of the most significant advances for cancer therapy in clinic. However, most of these therapies focused on stimulating the adaptive immune system-mediated elimination of tumor. Recent studies indicated that CD47/Signal-regulatory protein alpha (SIRPα), an innate anti-phagocytic axis between cancer cells and macrophages, could be a promising therapeutic target. Here, we review the current knowledge about developing CD47/SIRPα checkpoint inhibitors, avoiding potential side effect and designing optimal combination therapies, and highlight the key points for future clinical applications of CD47/SIRPα axis-targeted tumor immunotherapy.
An ecosystem approach for studying the impact of offshore wind farms: a French case study
Authors: Pezy Jean-Philippe , Raoux Aurore , Dauvin Jean-Claude 
Published: August 2018

Abstract
The French government is planning the construction of offshore wind farms (OWF) in the next decade (around 2900 MW). Following the European Environmental Impact Assessment Directive 85/337/EEC, several studies have been undertaken to identify the environmental conditions and ecosystem functioning at selected sites prior to OWF construction. However, these studies are generally focused on the conservation of some species and there is no holistic approach for analysing the effects arising from OWF construction and operation. The objective of this article is to promote a sampling strategy to collect data on the different ecosystem compartments of the future Dieppe-Le Tréport (DLT) wind farm site, adopting an ecosystem approach, which could be applied to other OWFs for the implementation of a trophic network analysis. For that purpose, an Ecopath model is used here to derive indices from Ecological Network Analysis (ENA) to investigate the ecosystem structure and functioning. The results show that the ecosystem is most likely detritus-based, associated with a biomass dominated by bivalves, which could act as a dead end for a classic trophic food web since their consumption by top predators is low in comparison to their biomass. The systemic approach developed for DLT OWF site should be applied for other French and European installations of Offshore Wind Farm.
Intradermal injection of Pythium insidiosum protein antigens for improved diagnosis and treatment of pythiosis in an experimental model
Authors: Weiblen Carla , Zanette Régis Adriel , Ribeiro Tatiana Corrêa , Pereira dos Santos Carlos Eduardo , Ianiski Lara Baccarin , Pereira Daniela Isabel Brayer , Santurio Janio Morais , Botton Sônia de Avila 
Published: August 2018

AbstractThe oomycetous pathogen Pythium insidiosum is the causative agent of pythiosis, a life-threatening disease that affects animals and humans. This infectious disease is difficult to treat, and early and accurate diagnosis is critical for effective treatment. In this sense, this study aimed to evaluate the intradermal (ID) injection of P. insidiosum protein antigens (PiPA) for the diagnosis and treatment of pythiosis using an experimental model. For diagnostic purposes, PiPA were injected by the ID route in the following groups of rabbits: (a) control; (b) previously immunized with PiPA injected by the subcutaneous (SC) route; and (c) infected with P. insidiosum zoospores. For treatment purposes, rabbits with pythiosis were also treated with PiPA by the ID or SC routes. Mean induration sizes were different at 24 h and 72 h readings when compared to the control group. Sensitivity of the protocol was 100% at 24 h and 80% at 72 h, with 100% specificity in both readings. PiPA treatment using ID or SC routes did not result in significant differences in lesion sizes and cure rates; however, serum levels of interferon-gamma were higher in SC route. This study demonstrates the applicability of PiPA ID for diagnosis and treatment of pythiosis in an experimental model.
Optimates/Populares
Authors: Rosillo-López Cristina 
Published: August 2018

Populares and optimates are two political denominations, especially used in ancient Roman politics during the 1st century bce during the Late Roman Republic (although the sources apply them sometimes to the 2nd century bce). The basis of such differentiation is Marcus Tullius Cicero (106–43 bce), Pro Sestio 96, which defined populares and optimates as two distinct political categories. Popularis (adjective, singular of the plural populares in Latin) is an ambiguous term: it could connote “pleasing to the people” or “in the interest of the people”; the term to define the opposite of the senatorial majority, a combination of a certain political strategy and a certain type of political eloquence (eloquentia popularis) or, finally, a certain political tradition. Many politicians termed populares were tribunes of the plebs and some of them died or were murdered in violent confrontations with the Senate. The term optimates, or boni (a similar term, not exactly a synonym), rarely occur in the sources. People ascribed to this group in modern scholarship are those who believed in senatorial authority and/or those supporting the interests of the wealthy. However, identification can be also problematic. Some of the main sources are Cicero, Pro Sestio 96 (takes a negative view; main locus of the confrontation optimates-populares); Sallust, Bellum Catilinae 20; Bellum Iugurthinum 31 (Memmius’s speech) and 85 (Marius’s speech); Historiae 1.55 (Lepidus’s speech) and 3.48 (Macer’s speech). Sallust’s Epistulae ad Caesarem have been considered to be both fake and authentic (latest edition Antonio Duplá, Guillermo Fatás, and Francisco Pina Polo, Rem publicam restituere: una propuesta popularis para la crisis republicana: las Epistulae ad Caesarem de Salustio [Zaragoza, Spain: Departamento de ciencias de la antigüedad Universidad de Zaragoza, 1994] considers them authentic). Best introductions in English: Zvi Yavetz, Plebs and princeps (New Brunswick, NJ: Transaction, 1988); Nicola Mackie, Popularis ideology and popular politics at Rome in the first century B. C. Rheinisches Museum für Philologie 135 (1992): 49–73; Margaret Robb, Beyond « populares » and « optimates »: political language in the late Republic (Stuttgart: Steiner, 2010); Antonio Duplá, “Consules populares,” in Consuls and res publica: holding high office in the Roman Republic, edited by Hans Beck, Antonio Duplá, Martin Jehne and Francisco Pina Polo (Cambridge, UK: Cambridge University Press, 2011), pp. 279–298; Claudia Tiersch, “Political Communication in the Late Roman Republic: Semantic Battles between Optimates and Populares?” in Institutions and Ideology in Republican Rome. Speech, Audience and Decision, edited by H. van der Blom, C. Gray and C. Steel (Cambridge, UK: Cambridge University Press, 2018), pp. 35–68.
Iranian Cinema
Authors: Kazemi Farshid 
Published: August 2018

Iranian cinema first came under international attention for its prerevolutionary art cinema known as the Iranian New Wave and more widely for its postrevolutionary cinematic movement called the New Iranian Cinema. However, Iran has had a longstanding history of cinema that began in 1900, with the introduction of film technology by the Qajar court photographer Ibrahim Khan Sani al-Saltaneh Akkasbashi. The development of cinema in Iran is inextricably linked to the development of modernity and the nation-state. The cinema in Iran was an important site where modernity (tajadud) and the nation (mellat) were respectively constructed, contested, and negotiated throughout the long 20th century and into the new millennium. The history of Iranian cinema is punctuated by the two revolutions in 20th-century Iran, namely the constitutional revolution of 1905–1911 and the later Islamic Revolution in 1979. Both of these events left an indelible mark on Iran and Iranian cinema, but none more so than the Islamic Revolution. In the second Pahlavi era and just before the 1979 revolution, along with the popular commercial cinema called filmfarsi (“Persian film”), Iranian cinema witnessed the development of art-house cinema or the Iranian New Wave (mowj-e now) as a reaction to this popular cinema, which was influenced by the aesthetics of Italian Neorealism and the French New Wave. But it is largely with the New Iranian Cinema of the postrevolutionary era that Iranian cinema received worldwide critical attention, wining regular awards at prestigious film festivals around the globe. After the 1979 revolution and the establishment of the Islamic Republic, new guidelines were established by the state apparatus to ensure that films produced in Iran were made according to the logic of an Islamic “system of modesty” (hejab in its broadest sense). Paradoxically, these censorship guidelines forced Iranian filmmakers to develop a new filmic grammar, which in a constant negotiation with state censors, contributed to a new visual and aural film form that is distinctive to Iranian cinema. In this way, the history of cinema in Iran can be divided into four distinct periods, from the Qajar era to the first Pahlavi period (1900–1941), the second Pahlavi era (1942–1979), the postrevolutionary era with the Islamization of Iranian cinema (1980–1988), and the emergence of the New Iranian Cinema (1990s and early 2000s). In the early 21st century, there is a subtle but visible shift away from the formal and narrative strategies of the New Iranian Cinema. It is too early at this stage to categorize the formal logic and aesthetics of this new iteration of Iranian cinema, as we are in the midst of its development, but if the New Iranian Cinema was recognizable under the sign of its master practitioner, Abbas Kiarostami (d. 2016), the new trend in Iranian cinema is perhaps under the visible influence of the two-time Oscar-winning director Asghar Farhadi.
Brief Report: HIV Pre-exposure Prophylaxis Engagement Among Adolescent Men Who Have Sex With Men: The Role of Parent–Adolescent Communication About Sex
Authors: Thoma Brian C. , Huebner David M. 
Published: August 2018

Background:
Adolescent men who have sex with men (AMSM) are severely affected by the HIV epidemic in the United States. Pre-exposure prophylaxis (PrEP) has proven extremely effective in preventing new HIV infections among adult men who have sex with men, but no research has examined PrEP awareness among AMSM. Furthermore, initial research investigating PrEP adherence among AMSM has found low adherence to the medication regimen. Effective parent–adolescent communication about sex is associated with safer sexual health behaviors among AMSM, and parent–adolescent communication is one potential avenue to increase PrEP engagement among AMSM.

Setting:
Participants included 636 AMSM in the United States who completed a cross-sectional online survey in 2015.

Methods:
Self-reported data on PrEP awareness, attitudes about PrEP, and perceived behavioral control for PrEP usage as well as frequency and quality of parent–adolescent communication about HIV were collected from AMSM. Regression models predicting PrEP awareness, attitudes, and perceived behavioral control from communication constructs were estimated, adjusting for demographic covariates.

Results:
Sixteen percent of AMSM were aware of PrEP. AMSM who reported more frequent communication about HIV with their parents were more likely to report being aware of PrEP. Among AMSM aware of PrEP, higher quality parent–adolescent communication about HIV was associated with higher perceived behavioral control for PrEP usage.

Conclusions:
Despite high HIV incidence among AMSM in the United States, PrEP awareness is low in this population. Effective parent–adolescent communication about HIV and sexual health could increase AMSM engagement with PrEP and enhance PrEP adherence within future trials among AMSM.
A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics
Authors: Jermiin Lars S , Catullo Renee A , Holland Barbara R 
Published: August 2018

Molecular phylogenetics plays a key role in comparative genomics and has an increasingly-significant impacts on science, industry, government, public health, and society. In this opinion paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence our phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness-of-fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.DedicationTo the memory of Rossiter H. Crozier (1943-2009), an evolutionary biologist, who, with his great generosity and wide-reaching inquisitiveness, inspired students and scientists in Australia, and abroad.
Female-biased embryonic death from genomic instability-induced inflammation
Authors: McNairn Adrian J. , Chuang Chen-Hua , Bloom Jordana C. , Wallace Marsha D. , Schimenti John C. 
Published: August 2018

AbstractGenomic instability (GIN) can trigger cellular responses including checkpoint activation, senescence, and inflammation. Though extensively studied in cell culture and cancer paradigms, little is known about the impact of GIN during embryonic development, a period of rapid cellular proliferation. We report that GIN-causing mutations in the MCM2-7 DNA replicative helicase render female mouse embryos to be dramatically more susceptible than males to embryonic lethality. This bias was not attributable to X-inactivation defects, differential replication licensing, or X vs Y chromosome size, but rather “maleness,” since XX embryos could be rescued by transgene-mediated sex reversal or testosterone (T) administration. The ability of exogenous or endogenous T to protect embryos was related to its anti-inflammatory properties. The NSAID ibuprofen rescued female embryos containing mutations not only in MCM genes but alsoFancm,which have elevated GIN from compromised replication fork repair. Additionally, deficiency for the anti-inflammatory IL10 receptor was synthetically lethal with the GIN-causingMcm4Chaos3helicase mutant. Our experiments indicate that embryonic and maternal GIN arising from DNA replication-associated DNA damage induces embryonic inflammation likely via the cGAS-STING response, preferentially killing female embryos while male embryos are protected by high levels of intrinsic T.
Haploinsufficiency of A20 impairs protein-protein interactome and leads into caspase-8-dependent enhancement of NLRP3 inflammasome activation
Authors: Rajamäki Kristiina , Keskitalo Salla , Seppänen Mikko , Kuismin Outi , Vähäsalo Paula , Trotta Luca , Väänänen Antti , Glumoff Virpi , Keskitalo Paula , Kaarteenaho Riitta , Jartti Airi , Hautala Nina , Jackson Päivi , Nordström Dan C , Saarela Janna , Hautala Timo , Eklund Kari K , Varjosalo Markku 
Published: August 2018

ABSTRACTObjectivesTNFAIP3encodes A20 that negatively regulates nuclear factor kappa light chain enhancer of activated B cells (NF-κB), the major transcription factor coordinating inflammatory gene expression.TNFAIP3polymorphisms have been linked with a spectrum of inflammatory and autoimmune diseases and recently, loss-of-function mutations in A20 were found to cause a novel inflammatory disease ‘haploinsufficiency of A20’ (HA20). Here we describe a family with HA20 caused by a novelTNFAIP3loss-of-function mutation and elucidate the upstream molecular mechanisms linking HA20 to dysregulation of NF-κB and the related inflammasome pathway.MethodsNF-κB activation was studied in a mutation-expressing cell line using luciferase reporter assay. Physical and close-proximity protein-protein interactions of wild-type andTNFAIP3p.(Lys91*) mutant A20 were analyzed using mass spectrometry. NF-κB –dependent transcription, cytokine secretion, and inflammasome activation were compared in immune cells of the HA20 patients and control subjects.ResultsThe protein-protein interactome of p.(Lys91*) mutant A20 was severely impaired, including inter-actions with proteins regulating NF-κB activation, DNA repair responses, and the NLR family pyrin domain containing 3 (NLRP3) inflammasome. The p.(Lys91*) mutant A20 failed to suppress NF-κB signaling, which led to increased NF-κB –dependent proinflammatory cytokine transcription. Functional experiments in the HA20 patients’ immune cells uncovered a novel caspase-8-dependent mechanism of NLRP3 inflammasome hyperresponsiveness that mediated the excessive secretion of interleukin-1β and -18.ConclusionsThe current findings significantly deepen our understanding of the molecular mechanisms underlying HA20 and other diseases associated with reduced A20 expression or function, paving the way for future therapeutic targeting of the pathway.
Learning dynamical information from static protein and sequencing data
Authors: Pearce Philip , Woodhouse Francis G. , Forrow Aden , Kelly Ashley , Kusumaatmaja Halim , Dunkel Jörn 
Published: August 2018

AbstractMany complex processes, from protein folding and virus evolution to brain activity and neuronal network dynamics, can be described as stochastic exploration of a high-dimensional energy landscape. While efficient algorithms for cluster detection and data completion in high-dimensional spaces have been developed and applied over the last two decades, considerably less is known about the reliable inference of state transition dynamics in such settings. Here, we introduce a flexible and robust numerical framework to infer Markovian transition networks directly from time-independent data sampled from stationary equilibrium distributions. Our approach combines Gaussian mixture approximations and self-consistent dimensionality reduction with minimal-energy path estimation and multi-dimensional transition-state theory. We demonstrate the practical potential of the inference scheme by reconstructing the network dynamics for several protein folding transitions, gene regulatory network motifs and HIV evolution pathways. The predicted network topologies and relative transition time scales agree well with direct estimates from time-dependent molecular dynamics data, stochastic simulations and phylogenetic trees, respectively. The underlying numerical protocol thus allows the recovery of relevant dynamical information from instantaneous ensemble measurements, effectively alleviating the need for time-dependent data in many situations. Owing to its generic structure, the framework introduced here will be applicable to high-throughput RNA and protein sequencing datasets and future cryo-electron-microscopy data, and can guide the design of new experimental approaches towards studying complex multiphase phenomena.