bluuebunny/crossref_metadata_2025 huggingface dataset:
Love and Caring
Authors: Jaworska Agnieszka , Wonderly Monique
Published: February 2020

Is there a principled framework for understanding the distinction between mere caring and love? This chapter critically assesses extant accounts, showing that the distinctive requirements for love that they propose are either insufficient or unnecessary. After identifying and exploring views that describe types of intimacy that suffice, but are too demanding to deem necessary, for love, this chapter develops a more ecumenical proposal for love’s distinctive character that unifies a central insight in the preceding views. On this proposal, the feature that is necessary and sufficient to distinguish love from mere caring is conceived in terms of love’s intimacy as reflected in a specific form of vulnerability. The lover, but not the mere carer, is subject to damage in her sense of herself as an agent leading a meaningful life directly in virtue of being permanently separated from the relevant object or in virtue of that object faring poorly.
Foundations of Religious Reform (Islah) and Cultural Revival (Nahda)
Authors: Hamzah Dyala
Published: February 2020

This chapter discusses the foundations of hegemonic reform and cultural revival discourses in the Arabic-speaking lands of the modern Middle East from the perspective of the most recent forays in scholarly fields such as Islamic and Ottoman studies. Teasing out periodization and geographies, it grounds the thought and practice of canonical and less canonical actors in the historical public sphere in which they operated, questioning the relationship between the Nahda and the Tanzimat, the Nahda and eighteenth-century revivalism, the Nahda and the seventeenth-century Arab-Islamic florescence, as well as the special status accorded “Islamic” reform within the Nahda. Finally, it probes the larger questions of modernity, subjectivity, and citizenship between the onset of the protectorates and the termination of the mandates, as these became encrypted within the major ideologies (pan-Islam, pan-Arabism, territorial nationalisms) and enacted through the most significant technologies mobilized by the actors (the press, the associations, the parties, and the schools).
Greek
Authors: Morales Helen
Published: February 2020

This article offers an overview of Greek literature of the Roman Empire. The first section discusses ways in which Greek writing responds to Roman rule. This section ranges widely and takes snapshots from six writers—Artemidorus, Plutarch, Lucian, Basil of Caesarea, Galen, and Josephus—from which to show the complexities involved in thinking about Greek literature and its attendant critical issues, including how we might read ‘resistance’ and how Hellenisms relate to Christianities, and Jewish and other identities. The second section focuses more closely on Greek poetry and pantomime, and the third section on the romance novels and Greek prose fiction, including a brief look at a couple of texts that possibly show Egyptian influences.
Theories of Language Contact
Authors: Winford Donald
Published: February 2020

This chapter depicts major theories of language contact, including those relating to the outcomes of borrowing, creole formation and other bilingual mixtures, with special emphasis on the framework proposed by Frans van Coetsem. This framework is multi-disciplinary in nature, built around linguistic, sociolinguistic, and psycholinguistic approaches. I first discuss the contributions of sociolinguistic approaches to our understanding of the ways in which social contexts and social factors influence the outcomes of language contact. I then evaluate various linguistic frameworks that have been proposed for describing the linguistic outcomes of language contact, the mechanisms involved, and the classification of contact phenomena. I argue that van Coetsem’s (1988, 2000) model of language contact offers a more consistent, accurate and principled explanation of the processes of change associated with different types of contact. Following that, I show how a wide variety of contact phenomena can be accounted for in terms of just two universal mechanisms of change—borrowing and imposition. Finally, I discuss ways in which psycholinguistic models of language production can contribute to our understanding of these mechanisms of contact-induced change.
Scraping the Web for Public Health Gains: Ethical Considerations from a ‘Big Data’ Research Project on HIV and Incarceration
Authors: Rennie Stuart , Buchbinder Mara , Juengst Eric , Brinkley-Rubinstein Lauren , Blue Colleen , Rosen David L
Published: February 2020

Web scraping involves using computer programs for automated extraction and organization of data from the Web for the purpose of further data analysis and use. It is frequently used by commercial companies, but also has become a valuable tool in epidemiological research and public health planning. In this paper, we explore ethical issues in a project that “scrapes” public websites of U.S. county jails as part of an effort to develop a comprehensive database (including individual-level jail incarcerations, court records and confidential HIV records) to enhance HIV surveillance and improve continuity of care for incarcerated populations. We argue that the well-known framework of Emanuel et al. (2000) provides only partial ethical guidance for the activities we describe, which lie at a complex intersection of public health research and public health practice. We suggest some ethical considerations from the ethics of public health practice to help fill gaps in this relatively unexplored area.
Patient-Reported Opioid Pill Consumption After an ED Visit: How Many Pills Are People Using?
Authors: McCarthy Danielle M , Kim Howard S , Hur Scott I , Lank Patrick M , Arroyo Christine , Opsasnick Lauren A , Piserchia Katherine , Curtis Laura M , Wolf Michael S , Courtney D Mark
Published: February 2020

Objectives

Recent guidelines advise limiting opioid prescriptions for acute pain to a three-day supply; however, scant literature quantifies opioid use patterns after an emergency department (ED) visit. We sought to describe opioid consumption patterns after an ED visit for acute pain.

Design

Descriptive study with data derived from a larger interventional study promoting safe opioid use after ED discharge.

Setting

Urban academic emergency department (>88,000 annual visits).

Subjects

Patients were eligible if age >17 years, not chronically using opioids, and newly prescribed hydrocodone-acetaminophen and were included in the analysis if they returned the completed 10-day medication diary.

Methods

Patient demographics and opioid consumption are reported. Opioid use is described in daily number of pills and daily morphine milligram equivalents (MME) both for the sample overall and by diagnosis.

Results

Two hundred sixty patients returned completed medication diaries (45 [17%] back pain, 52 [20%] renal colic, 54 [21%] fracture/dislocation, 40 [15%] musculoskeletal injury [nonfracture], and 69 [27%] “other”). The mean age (SD) was 45 (15) years, and 59% of the sample was female. A median of 12 pills were prescribed. Patients with renal colic used the least opioids (total pills: median [interquartile range {IQR}] = 3 [1–7]; total MME: median [IQR] = 20 [10–50]); patients with back pain used the most (total pills: median [IQR] = 12 [7–16]; total MME: median [IQR] = 65 [47.5–100]); 92.5% of patients had leftover pills.

Conclusions

In this sample, pill consumption varied by illness category; however, overall, patients were consuming low quantities of pills, and the majority had unused pills 10 days after their ED visit.
Assessing the use and understanding of the Portuguese heat–health warning system (ÍCARO)
Authors: Leite A , Santos A J , Silva S , Nunes B , Mexia R , Rodrigues A P
Published: February 2020

Background

Heatwaves can lead to increased mortality. In the Portuguese heat–health warning system (HHWS), ÍCARO, a daily report with heat-related mortality prediction is sent to heat–health action plan (HHAP) practitioners. HHAP practitioners assess risk and implement measures to prevent heatwave-related impact, but ÍCARO’s use and understanding are unknown. We assessed ÍCARO’s use and understanding by key HHAP practitioners.

Methods

We conducted semi-structured interviews with national/regional HHAP practitioners. Interviews were recorded, transcribed and analysed using thematic content analysis. To maximize credibility a validation process was implemented through researcher triangulation; a sample of 30 segments was recorded by independent researchers.

Results

We conducted six interviews with nine professionals (mean time 52 min) from five regions. We identified four categories: report’s content and presentation, report’s reception and communication, ÍCARO and risk assessment and other issues. Practitioners use ÍCARO and perceived it as relevant; they raised issues on its interpretation and felt these were not fully addressed, given researchers’ use of statistical/epidemiological terms. We identified the need for improved communication and report’s clarity.

Conclusions

Our study stresses the need for collaboration between experts within HHWS/HHAP. Despite ÍCARO’s understanding being challenging, practitioners consider it a relevant tool. Researchers should use less statistical language and clarify ÍCARO’s interpretation. Practitioners’ needs should be considered when developing/revising tools.
Do penguins’ vocal sequences conform to linguistic laws?
Authors: Favaro Livio , Gamba Marco , Cresta Eleonora , Fumagalli Elena , Bandoli Francesca , Pilenga Cristina , Isaja Valentina , Mathevon Nicolas , Reby David
Published: February 2020

Information compression is a general principle of human language: the most frequent words are shorter in length (Zipf's Law of Brevity) and the duration of constituents decreases as the size of the linguistic construct increases (Menzerath–Altmann Law). Vocal sequences of non-human primates have been shown to conform to both these laws, suggesting information compression might be a more general principle. Here, we investigated whether display songs of the African penguin, which mediate recognition, intersexual mate choice and territorial defence, conform with these laws. Display songs are long, loud sequences combining three types of syllables. We found that the shortest type of syllable was the most frequent (with the shortest syllable being repeated stereotypically, potentially favouring signal redundancy in crowded environments). We also found that the average duration of the song's constituents was negatively correlated with the size of the song (a consequence of increasing the relative number of the shortest syllable type, rather than reducing the duration across all syllable types, thus preserving the communication of size-related information in the duration of the longest syllable type). Our results provide the first evidence for conformity to Zipf's and Menzerath–Altmann Laws in the vocal sequences of a non-primate species, indicating that these laws can coexist with selection pressures specific to the species' ecology.
Prehistoric baseline reveals substantial decline of oyster reef condition in a Gulf of Mexico conservation priority area
Authors: Hesterberg Stephen G. , Herbert Gregory S. , Pluckhahn Thomas J. , Harke Ryan M. , Al-Qattan Nasser M. , Duke C. Trevor , Moore Evan W. , Smith Megan E. , Delgado Alexander C. , Sampson Christina P.
Published: February 2020

The Gulf of Mexico (GoM) is home to the world's largest remaining wild oyster fisheries, but baseline surveys needed to assess habitat condition are recent and may represent an already-shifted reference state. Here, we use prehistoric oysters from archaeological middens to show that oyster size, an indicator of habitat function and population resilience, declined prior to the earliest assessments of reef condition in an area of the GoM previously considered pristine. Stable isotope sclerochronlogy reveals extirpation of colossal oysters occurred through truncated life history and slowed growth. More broadly, our study suggests that management strategies affected by shifting baselines may overestimate resilience and perpetuate practices that risk irreversible decline.
Constraining classifiers in molecular analysis: invariance and robustness
Authors: Lausser Ludwig , Szekely Robin , Klimmek Attila , Schmid Florian , Kestler Hans A.
Published: February 2020

Analysing molecular profiles requires the selection of classification models that can cope with the high dimensionality and variability of these data. Also, improper reference point choice and scaling pose additional challenges. Often model selection is somewhat guided byad hocsimulations rather than by sophisticated considerations on the properties of a categorization model. Here, we derive and report four linked linear concept classes/models with distinct invariance properties for high-dimensional molecular classification. We can further show that these concept classes also form a half-order of complexity classes in terms of Vapnik–Chervonenkis dimensions, which also implies increased generalization abilities. We implemented support vector machines with these properties. Surprisingly, we were able to attain comparable or even superior generalization abilities to the standard linear one on the 27 investigated RNA-Seq and microarray datasets. Our results indicate thata priorichosen invariant models can replacead hocrobustness analysis by interpretable and theoretically guaranteed properties in molecular categorization.
Criticality of plasma membrane lipids reflects activation state of macrophage cells
Authors: Cammarota Eugenia , Soriani Chiara , Taub Raphaelle , Morgan Fiona , Sakai Jiro , Veatch Sarah L. , Bryant Clare E. , Cicuta Pietro
Published: February 2020

Signalling is of particular importance in immune cells, and upstream in the signalling pathway many membrane receptors are functional only as complexes, co-locating with particular lipid species. Work over the last 15 years has shown that plasma membrane lipid composition is close to a critical point of phase separation, with evidence that cells adapt their composition in ways that alter the proximity to this thermodynamic point. Macrophage cells are a key component of the innate immune system, are responsive to infections and regulate the local state of inflammation. We investigate changes in the plasma membrane’s proximity to the critical point as a response to stimulation by various pro- and anti-inflammatory agents. Pro-inflammatory (interferonγ, Kdo 2-Lipid A, lipopolysaccharide) perturbations induce an increase in the transition temperature of giant plasma membrane vesicles; anti-inflammatory interleukin 4 has the opposite effect. These changes recapitulate complex plasma membrane composition changes, and are consistent with lipid criticality playing a master regulatory role: being closer to critical conditions increases membrane protein activity.
James Petiver's ‘joynt-stock’: middling agency in urban collecting networks
Authors: Marples Alice
Published: February 2020

This article explores the complexities of James Petiver and Hans Sloane's relationship with one another and their shared contacts, examining the ways in which their networks overlapped but also, crucially, differed from one another. It shows that, though they had common interests and institutional memberships, Petiver ultimately occupied a different urban world from Sloane, a middling, trade-orientated stratum of society with its own forms of sociability and business, credit and advancement. It was this position that helped Petiver bridge a range of gaps in elite scholarly exchange, making himself indispensable through his effective mediation between different urban groups and access to spaces beyond Sloane's reach. It argues that greater attention needs to be paid to the imbrication of middling interests and agencies that operated across London's natural history communities, in order to prompt us to think more carefully about the strategies and interests of those who tried to navigate them.
Cold call: the acoustic repertoire of Ross Sea killer whales (Orcinus orca,Type C) in McMurdo Sound, Antarctica
Authors: Wellard Rebecca , Pitman Robert L. , Durban John , Erbe Christine
Published: February 2020

Killer whales (Orcinus orca) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 h of recordings, 6386 killer whale vocalizations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls were examined for characteristic patterns yielding a catalogue of 28 call types (comprising 1250 calls). Acoustic parameters of each call were measured and summarized by call type. Type C killer whales produced complex calls, consisting of multiple frequency-modulated, amplitude-modulated and pulsed components. Often, two components occurred simultaneously, forming a biphonation; although the biphonic components did not necessarily start and end together, with one component lasting over several others. The addition and deletion of components yielded call subtypes. Call complexity appears stable over time and may be related to feeding ecology. Characterization of the Type C acoustic repertoire is an important step for the development of passive acoustic monitoring of the diverse assemblage of killer whale ecotypes in Antarctica's rapidly changing marine ecosystems.
Quantum chemical molecular dynamics and metadynamics simulation of aluminium binding to amyloid-β and related peptides
Authors: Platts James A.
Published: February 2020

We report semi-empirical tight-binding simulations of the interaction between Al(III) and biologically relevant peptides. The GFN2-XTB method is shown to accurately reproduce previously reported and density functional theory (DFT)-calculated geometries of model systems. Molecular dynamics simulations based on this method are able to sample peptide flexibility over timescales of up to nanoseconds, but these timescales are insufficient to explore potential changes in metal–peptide binding modes. To achieve this, metadynamics simulations using root mean square deviation as a collective variable were employed. With suitably chosen biasing potentials, these are able to efficiently explore diverse coordination modes, for instance, through Glu and/or Asp residues in a model peptide. Using these methods, we find that Al(III) binding to the N-terminal sequence of amyloid-β is highly fluxional, with all acidic sidechains and several backbone oxygens participating in coordination. We also show that such simulations could provide a means to predict
a priori
possible binding modes as a precursor to longer, atomistic simulations.
Why does
D
= 4, rather than more (or less)? An Orwellian explanation
Authors: Deser S.
Published: February 2020

Two simple, if draconian, assumptions about classical gravity actions fix space–time’s dimension at
D
 = 4.
Diet contributes to urban-induced alterations in gut microbiota: experimental evidence from a wild passerine
Authors: Teyssier Aimeric , Matthysen Erik , Hudin Noraine Salleh , de Neve Liesbeth , White Joël , Lens Luc
Published: February 2020

Urban sprawl increasingly affects the ecology of natural populations, including host–microbiota interactions, with observed differences in the gut microbiota between urban and rural hosts. While different mechanisms could explain this pattern, dietary uptake constitutes a likely candidate. To assess the contribution of diet in explaining urban–rural variation in gut microbiota, we performed an aviary experiment in which urban and rural house sparrows were fed with mimics of urban or rural diets. Before the experiment, rural sparrows hosted more diverse gut communities, with a higher relative abundance of Enterococcaceae and Staphylococcaceae and lower abundance of genes involved in xenobiotic degradation and lipid metabolism than their urban counterparts. The experimental diets significantly altered gut microbiota α- and β-diversity and taxonomic composition, with the strongest shifts occurring in individuals exposed to contrasting diets. Overall, diet-induced shifts resembled initial differences between free-ranging urban and rural hosts. Furthermore, rural diet had a positive impact on urban host body mass but only in hosts with the highest initial gut diversity. Overall, our results indicate that diet constitutes an important factor contributing to differences in gut microbiota along the urbanization gradient and provide new insights on possible fitness consequences of a reduced gut diversity in urban settings.
Effect of four kinds of complexing iron on the process of iron uptake by Anabaena flos-aquae
Authors: Qiu Yongting , Wang Zhihong , Huang Ziqi , Liu Feng , Tang Daijun , Liu Junxia
Published: February 2020

Abstract

Iron (Fe), which is a necessary micronutrient for algal growth, plays an important role in the physiological metabolism and enzymatic reactions of algae. This study aimed to investigate the absorption process of four kinds of complexing iron absorbed by Anabaena flos-aquae. Results showed that the absorptive capacity of A. flos-aquae to complex iron was inversely proportional to the stability of the complex bond of complex iron. Complex iron with weak binding ability can be quickly adsorbed by A. flos-aquae. The absorptive rate was as follows: ferric humate, ferric oxalate >ammonium ferric citrate >EDTA Fe. For EDTA-Fe with a strong binding ability, a moderate iron concentration (e.g. 0.6 mg l−1) is favourable for iron uptake by A. flos-aquae. Our experiments also revealed that the process of separating iron from complex iron before entering algal cells was probably as follows: iron complexed with organic ligands were firstly adsorbed on the surface of algae cells; afterwards, iron ions were captured by organic matter on the surface of algae cells, accompanied by the rupture of the bond between Fe3+ and ligand; finally, the Fe3+ entered into the cell of algae while the organic ligands returned to the medium.
Scrutinizing surface glycoproteins and poxin-schlafen protein to design a heterologous recombinant vaccine against monkeypox virus
Authors: Hoque Syeda Farjana , Bappy Md. Nazmul Islam , Chowdhury Anjum Taiebah , Parvez Md. Sorwer Alam , Ahmed Foeaz , Imran Md. Abdus Shukur , Azim Kazi Faizul , Hasan Mahmudul
Published: February 2020

Monkeypox is a zoonotic disease caused by monkeypox virus with noteworthy mortality and morbidity. Several recent outbreaks and the need of dependable reconnaissance have raised the level of concern for this developing zoonosis. In the present study, a reverse vaccinology strategy was developed to construct a peptide vaccine against monkeypox virus by exploring cell surface binding protein, Poxin-Schlafen andenvelope protein. Both humoral and cell mediated immunity induction were the main concerned properties for the designed peptide vaccine. Therefore, both T cell and B cell immunity against monkeypox virus were analyzed from the conserver region of the selected protein. Antigenicity testing, transmembrane topology screening, allergenicity and toxicity assessment, population coverage analysis and molecular docking approach were used to create the superior epitopes of moneypox virus. The subunit vaccine was constructed using highly immunogenic epitopes with appropriate adjuvant and linkers. Molecular docking examination of the refined vaccine with various MHCs and human immune receptor illustrated higher binding interaction. The designed construct was reverse transcribed and adjusted forE. colistrain K12 earlier to inclusion inside pET28a(+) vector for its heterologous cloning and expression. The study could start in vitro and in vivo studies concerning effective vaccine development against monkeypox virus.
Machine intelligence design of 2019-nCoV drugs
Authors: Gao Kaifu , Nguyen Duc Duy , Wang Rui , Wei Guo-Wei
Published: February 2020

Wuhan coronavirus, called 2019-nCoV, is a newly emerged virus that infected more than 9692 people and leads to more than 213 fatalities by January 30, 2020. Currently, there is no effective treatment for this epidemic. However, the viral protease of a coronavirus is well-known to be essential for its replication and thus is an effective drug target. Fortunately, the sequence identity of the 2019-nCoV protease and that of severe-acute respiratory syndrome virus (SARS-CoV) is as high as 96.1%. We show that the protease inhibitor binding sites of 2019-nCoV and SARS-CoV are almost identical, which means all potential anti-SARS-CoV chemotherapies are also potential 2019-nCoV drugs. Here, we report a family of potential 2019-nCoV drugs generated by a machine intelligence-based generative network complex (GNC). The potential effectiveness of treating 2019-nCoV by using some existing HIV drugs is also analyzed.
Understanding Adaptive Immune System as Reinforcement Learning
Authors: Kato Takuya , Kobayashi Tetsuya J.
Published: February 2020

The adaptive immune system of vertebrates can detect, respond to, and memorize diverse pathogens from past experience. While the selection of T helper (Th) clones is the simple and established mechanism to recognize and memorize new pathogens, the question that still remains unexplored is how the Th cells can acquire better ways to bias the responses of immune cells for eliminating pathogens more efficiently by translating the recognized antigen information into regulatory signals. In this work, we address this problem by associating the adaptive immune network organized by the Th cells with reinforcement learning (RL). By employing recent advancements of network-based RL, we show that the Th immune network can acquire the association between antigen patterns of and the effective responses to pathogens. Moreover, the clonal selection as well as other inter-cellular interactions are derived as a learning rule of this network. We also demonstrate that the stationary clone-size distribution after learning shares characteristic features with those observed experimentally. Our theoretical framework may contribute to revising and renewing our understanding of adaptive immunity as a learning system.
Integrative Bioinformatics Analysis Provides Insight into the Molecular Mechanisms of 2019-nCoV
Authors: He Xiang , Zhang Lei , Ran Qin , Wang Junyi , Xiong Anying , Wu Dehong , Chen Feng , Li Guoping
Published: February 2020

The 2019-nCoV is reported to share the same entry (ACE2) as SARS-CoV according to the updated findings. Analyzing the distribution and expression level of the route of coronavirus may help reveal underlying mechanisms of viral susceptibility and post-infection modulation. In this study, we found that the expression of ACE2 in healthy populations and patients with underlying diseases was not significantly different, suggesting relatively similar susceptibility. Besides, based on the expression of ACE2 in smoking individuals, we inferred that long-term smoking might be a risk factor for 2019-nCoV. Analyzing the ACE2 in SARS-CoV infected cells suggested that ACE2 was more than just a receptor but also participated in post-infection regulation, including immune response, cytokine secretion, and viral genome replication. Moreover, we also constructed Protein-protein interaction (PPI) networks and identified hub genes in viral activity and cytokine secretion. Our findings may explain the clinical symptoms so far and help clinicians and researchers understand the pathogenesis and design therapeutic strategies for 2019-nCoV.
Getting to zero quickly in the 2019-nCov epidemic with vaccines or rapid testing
Authors: Chowell Gerardo , Dhillon Ranu , Srikrishna Devabhaktuni
Published: February 2020

Any plan for stopping the ongoing 2019-nCov epidemic must be based on a quantitative understanding of the proportion of the at-risk population that needs to be protected by effective control measures in order for transmission to decline sufficiently and quickly enough for the epidemic to end. Using an SEIR-type transmission model, we contrasted two alternate strategies by modeling the proportion of the population that needs to be protected from infection by one-time vaccination (assuming 100% effectiveness) or by testing with isolation and treatment of individuals within six, 24, or 48 hours of symptom onset. If R is currently 2.2, vaccination at the herd immunity coverage of 55% would drive R just below 1, but transmission could persist for years. Over 80% of coverage is required to end the epidemic in 6 months with population-wide vaccination. The epidemic could be ended in just under a year if testing with isolation and treatment reached 80% of symptomatically infected patients within 24 hours of symptom onset (assuming 10% asymptomatic transmission). The epidemic could be ended in six months if testing with isolation and treatment reached 90% of symptomatic patients. If 90% of symptomatic patients could be tested within six hours of symptoms appearing, the epidemic could be ended in under four months.
Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation
Authors: Beleggia Romina , Omranian Nooshin , Holtz Yan , Gioia Tania , Fiorani Fabio , Nigro Franca M. , Pecchioni Nicola , De Vita Pasquale , Schurr Urlich , David Jaques , Nikoloski Zoran , Papa Roberto
Published: February 2020

Mounting evidence indicates the key role of Nitrogen (N) on diverse processes in plant, including not only yield but also development and defense. Using a combined transcriptomics and metabolomics approach, we studied the response of seedlings to N starvation of two different tetraploid wheat genotypes from the two main domesticated subspecies, emmer (Triticum turgidumssp.dicoccum) and durum wheat (Triticum turgidumssp.durum). We found that durum wheat exhibits broader and stronger response in comparison to emmer as evidenced by the analysis of the differential expression pattern of both genes and metabolites and gene enrichment analysis. Emmer and durum wheat showed major differences in the responses to N starvation for transcription factor families. While emmer showed differential reduction in the levels of primary metabolites to N starvation, durum wheat exhibited increased levels of most metabolites, including GABA as an indicator of metabolic imbalance. The correlation-based networks including the differentially expressed genes and metabolites revealed tighter regulation of metabolism in durum wheat in comparison to emmer, as evidenced by the larger number of significant correlations. We also found that glutamate and GABA had highest values of centrality in the metabolic correlation network, suggesting their critical role in the genotype-specific response to N starvation of emmer and durum wheat, respectively. Moreover, this finding indicates that there might be contrasting strategies associated to GABA and Glutamate signaling modulating shootvsroot growth in the two different wheat subspecies.
Triacylglycerol synthesis enhances macrophage inflammatory function
Authors: Castoldi Angela , Monteiro Lauar B , van Teijlingen Bakker Nikki , Sanin David E , Rana Nisha , Corrado Mauro , Cameron Alanna M , Hässler Fabian , Matsushita Mai , Caputa George , Klein Geltink Ramon I. , Büscher Jörg , Edwards-Hicks Joy , Pearce Erika L , Pearce Edward J
Published: February 2020

Macrophages are integral to most tissues. Foam cells, macrophages with lipid droplets (LDs) which are stores of triacylglycerols (TGs) and cholesterol esters (CEs), are found in various disease states1. LDs can act as energy stores since TG lipolysis releases fatty acids (FAs) for mitochondrial oxidation (FAO), a process that relies on long-chain FA conversion into acylcarnitines by the enzyme Cpt1a2. However, in macrophages, proinflammatory signals result in diminished FAO and increased TG synthesis with LD development3,4. We explored the significance of LDs in cells that do not utilize FAO. We show that macrophages stimulated with lipopolysaccharide (LPS) plus interferon-γ (IFNγ) accumulate TGs in LDs, and long-chain acylcarnitines. In these cells, inhibition of TG synthesis results in diminished LD development, and increased long chain acylcarnitine levels, suggesting that FA fate is balanced between TG and acylcarnitine synthesis. Nevertheless, TG-synthesis is required for inflammatory macrophage function, since its inhibition negatively affects production of proinflammatory IL-1β, IL-6 and PGE2, and phagocytic capacity, and protects against LPS-induced shock in vivo. Failure to make PGE2 is critical for this phenotype, since exogenous PGE2 reverses the anti-inflammatory effects of TG-synthesis inhibition. These findings place LDs in a position of central functional importance in inflammatory macrophages.
Aridity drives coordinated trait shifts but not decreased trait variance across the geographic range of eight Australian trees
Authors: Anderegg Leander DL , Loy Xingwen , Markham Ian P. , Elmer Christina M , Hovenden Mark J , Lambers Janneke Hille Ris , Mayfield Margaret M
Published: February 2020

Context

Large intraspecific functional trait variation strongly impacts many aspects of natural communities and ecosystems, yet is inconsistent across traits and species.

Approach

We measured within-species variation in leaf mass per area (LMA), leaf dry matter content (LDMC), branch wood density (WD), and allocation to stem area vs. leaf area in branches (branch Huber value, HV) across the aridity range of seven Australian eucalypts and anAcaciaspecies to explore how traits and their variances change with aridity.

Results and Conclusions

Within-species, we found consistent increases in LMA, LDMC and WD, and HV with increasing aridity, resulting in consistent trait coordination across tissues. However, this coordination only emerged across sites with large climate differences. Unlike trait means, patterns of trait variance with aridity were mixed across populations and species and showed limited support for constrained trait variation in dryer populations or more xeric species.

Synthesis

Our results highlight that climate can drive consistent within-species trait patterns, but that these patterns might often be obscured by the complex nature of morphological traits and sampling incomplete species ranges or sampling confounded stress gradients.
Oral Pretreatment with Galantamine Effectively Mitigates the Acute Toxicity of a Supra-Lethal Dose of Soman in Cynomolgus Monkeys Post-treated with Conventional Antidotes
Authors: Lane Malcolm , Carter D’Arice , Pescrille Joseph D. , Aracava Yasco , Fawcett William P. , Basinger G.W. , Pereira Edna F.R. , Albuquerque Edson X.
Published: February 2020

The present study was designed to evaluate the effectiveness of galantamine administered orally as a pre-treatment to mitigate the acute toxicity of 4.0xLD50 soman in Cynomolgus monkeys post-treated with atropine, 2-PAM, and midazolam. Pharmacokinetic experiments revealed that the oral doses of 1.5 and 3.0 mg/kg galantamine HBr were quickly absorbed and produced plasma concentrations of galantamine that generated approximately 20% to 40% reversible inhibition of blood acetylcholinesterase (AChE) activity. This degree of reversible AChE inhibition has been shown to be safe and sufficient to protect AChE from the irreversible inhibition by nerve agents, and, thereby, suppress the acute toxicity of these agents. Thus, in subsequent experiments, adult male Cynomolgus monkeys were pretreated orally with 1.5 or 3.0 mg/kg galantamine, challenged intramuscularly with 4.0xLD50, and post-treated with intramuscular injections of 0.4 mg/kg atropine, 30 mg/kg 2-PAM, and 0.32 mg/kg midazolam. All animals subjected to these treatments survived the soman. By contrast, none of the animals that were pretreated with saline and only 40% of the animals that were pretreated with pyridostigmine survived the soman challenge when post-treated with the same conventional antidotal therapy as that delivered to the galantamine-pretreated, soman-challenged monkeys. In addition, large numbers of degenerating neurons were visualized in the hippocampi of soman-challenged monkeys that had been pretreated with pyridostigmine or saline, but not in the hippocampi of animals that had been pretreated with galantamine. To our knowledge, this is the first study to demonstrate the effectiveness of clinically relevant oral doses of galantamine to prevent the acute toxicity of supra-lethal doses of soman in non-human primates.
Morphological description of the male genital organs ofPontoporia blainvillei(Gervais & d’Orbigny, 1844)
Authors: Randi Caroline Bizarre , Spinelli Lucas Guedes , de Britto Mari Renata , de Souza Ramos Angrimani Daniel , Bertozzi Carolina Pacheco , Plácido Guimarães Juliana
Published: February 2020

Pontoporia blainvilleior Franciscana is a small cetacean endemic of South Atlantic Ocean and its highlighted as the most endangered species. Despite the necessity to development conservation strategies forPontoporia blainvilleistudies aiming to feature the reproductive biology and morphological characteristics of the genital organs are still scarce. In this context, the aim of this study was describe the morphological aspects of the genital organs ofPontoporia blainvillei. For this purpose, six male specimens ofP. blainvilleistranded on the southeast region of Brazil, were used. Initially animals were measured, and the genital organs were collected, dissected and photodocumented. Then, fragments of all collected organs were submitted to microscopic analysis. The male genital organs ofP. blainvilleishowed similar results described for other cetaceans, such as, topography in abdominal cavity, presence of two testicles with epididymis, fibroelastic penis with sigmoid shape and presence of deferent duct. Moreover, a male uterus non-functional, two vestigial bones that support the penis, one retractor penis muscle and presence of associated muscles that support the entire reproductive apparatus were observed. However, some differences were present, such as, a simple cubic epithelium in the light of the epididymis, a small testicle even in sexually mature animals and absence of prostate, not previously observed in other cetaceans. Therefore, the animals analyzed showed similar features to other cetaceans, however some peculiarities were observed.
What do blind people “see” with retinal prostheses? Observations and qualitative reports of epiretinal implant users
Authors: Erickson-Davis Cordelia , Korzybska Helma
Published: February 2020

Introduction: Retinal implants have now been approved and commercially available for certain clinical populations for over 5 years, with hundreds of individuals implanted, scores of them closely followed in research trials. Despite these numbers, however, few data are available that would help us answer basic questions regarding the nature and outcomes of artificial vision: what do participants see when the device is turned on for the first time, and how does that change over time?

Methods: Semi-structured interviews and observations were undertaken at two sites in France and the UK with 16 participants who had received either the Argus II or IRIS II devices. Data were collected at various time points in the process that implant recipients went through in receiving and learning to use the device, including initial evaluation, implantation, initial activation and systems fitting, re-education and finally post-education. These data were supplemented with data from interviews conducted with vision rehabilitation specialists at the clinical sites and clinical researchers at the device manufacturers (Second Sight and Pixium Vision). Observational and interview data were transcribed, coded and analyzed using an approach guided by Interpretative Phenomenological Analysis (IPA).

Results: Implant recipients described the perceptual experience produced by their epiretinal implants as fundamentally, qualitatively different than natural vision. All used terms that invoked electrical stimuli to describe the appearance of their percepts, yet the characteristics used to describe the percepts varied significantly between participants. Artificial vision for these participants was a highly specific, learned skill-set that combined particular bodily techniques, associative learning and deductive reasoning in order to build a “lexicon of flashes” - a distinct perceptual vocabulary that they then used to decompose, recompose and interpret their surroundings. The percept did not transform over time; rather, the participant became better at interpreting the signals they received. The process of using the device never ceased to be cognitively fatiguing, and did not come without risk or cost to the participant. In exchange, participants received hope and purpose through participation, as well as a new kind of sensory signal that may not have afforded practical or functional use in daily life but, for some, provided a kind of “contemplative perception” that participants tailored to individualized activities.

Conclusion: Attending to the qualitative reports of participants regarding the experience of artificial vision provides valuable information not captured by extant clinical outcome measures. These data can both inform device design and rehabilitative techniques, as well as grant a more holistic understanding of the phenomenon of artificial vision.
Beef cattle that respond differently to fescue toxicosis have distinct gastrointestinal tract microbiota
Authors: Koester Lucas R , Poole Daniel H , Serão Nick VL , Schmitz-Esser Stephan
Published: February 2020

Tall fescue (Lolium arundinaceum) is a widely used forage grass which shares a symbiosis with the endophytic fungusEpichloë coenophiala. The endophyte produces an alkaloid toxin that provides herbivory, heat and drought resistance to the grass, but can cause fescue toxicosis in grazing livestock. Fescue toxicosis can lead to reduced weight gain and milk yields resulting in significant losses to the livestock industry. In this trial, 149 Angus cows across two farms were continuously exposed to toxic, endophyte-infected, fescue for a total of 13 weeks. Of those 149 cows, 40 were classified into either high (HT) or low (LT) tolerance groups according to their growth performance (weight gain). 20 HT and 20 LT cattle balanced by farm were selected for 16S rRNA gene and ITS1 region Illumina MiSeq amplicon sequencing to compare the fecal microbiota of the two tolerance groups. This study reveals significantly (P<0.05) different bacterial and fungal microbiota between HT and LT cattle, and indicates that fungal phylotypes may be important for an animal’s response to fescue toxicosis: We found that fungal phylotypes affiliating to the Neocallimastigaceae, which are known to be important fiber-degrading fungi, were consistently more abundant in the HT cattle. Whereas fungal phylotypes related to the genusTheleboluswere more abundant in the LT cattle. This study also found more pronounced shifts in the microbiota in animals receiving higher amounts of the toxin. We identified fungal phylotypes which were consistently more abundant either in HT or LT cattle and may thus be associated with the respective animal’s response to fescue toxicosis. Our results thus suggest that some fungal phylotypes might be involved in mitigating fescue toxicosis. The results of our study provide a basis for investigating the functional role of the gastrointestinal microbiota in fescue toxicosis in more detail in the future.
Prior hypoxia exposure enhances murine microglial inflammatory gene expressionin vitrowithout concomitant H3K4me3 enrichment
Authors: Kiernan Elizabeth A. , Ewald Andrea C. , Ouellette Jonathan N. , Wang Tao , Roopra Avtar , Watters Jyoti J.
Published: February 2020

Hypoxia is a component of multiple disorders, including stroke and sleep-disordered breathing, that often precede or are comorbid with neurodegenerative diseases. However, little is known about how hypoxia affects the ability of microglia, resident CNS macrophages, to respond to subsequent inflammatory challenges that are often present during neurodegenerative processes. We therefore tested the hypothesis that hypoxia would enhance or “prime” microglial pro-inflammatory gene expression in response to a later inflammatory challenge without programmatically increasing basal levels of pro-inflammatory cytokine expression. To test this, we pre-exposed immortalized N9 and primary microglia to hypoxia (1% O2) for 16 hrs and then challenged them with pro-inflammatory lipopolysaccharide (LPS) either immediately or 3-6 days following hypoxic exposure. We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to analyze primed microglial inflammatory gene expression and modifications to histone H3 lysine 4 trimethylation (H3K4me3) at the promoters of primed genes. We found that microglia exhibited enhanced responses to LPS 3 days and 6 days post-hypoxia. Surprisingly however, the majority of primed genes were not enriched for H3K4me3 acutely following hypoxia exposure. Using the bioinformatics tool MAGICTRICKS and reversible pharmacological inhibition, we found that primed genes required the transcriptional activities of NF-ĸB. These findings provide evidence that hypoxia pre-exposure could lead to persistent and aberrant inflammatory responses in the context of CNS disorders.
Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies
Authors: Ahmed Syed Faraz , Quadeer Ahmed A. , McKay Matthew R.
Published: February 2020

The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an imminent need to better understand this new virus and to develop ways to control its spread. In this study, we sought to gain insights for vaccine design against SARS-CoV-2 by considering the high genetic similarity between SARS-CoV-2 and SARS-CoV, which caused the outbreak in 2003, and leveraging existing immunological studies of SARS-CoV. By screening the experimentally-determined SARS-CoV-derived B cell and T cell epitopes in the immunogenic structural proteins of SARS-CoV, we identified a set of B cell and T cell epitopes derived from the spike (S) and nucleocapsid (N) proteins that map identically to SARS-CoV-2 proteins. As no mutation has been observed in these identified epitopes among the available SARS-CoV-2 sequences (as of 9 February 2020), immune targeting of these epitopes may potentially offer protection against this novel virus. For the T cell epitopes, we performed a population coverage analysis of the associated MHC alleles and proposed a set of epitopes that is estimated to provide broad coverage globally, as well as in China. Our findings provide a screened set of epitopes that can help guide experimental efforts towards the development of vaccines against SARS-CoV-2.