bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective Variations of related Physicochemical Properties of Nucleotides Leading to Amino Acids for Characterizing Genes and Proteins
Authors: Sengupta Antara , Choudhury Pabitra Pal 
Published: May 2018

AbstractThe aim of this paper is to make quantitative analysis of the properties which is really being carried from DNA sequence and finally landing up to the properties of a protein structure through its primary protein sequence. Thus, the paper has a theory which is applicable for any arbitrary DNA sequence whether it is of various species or mutated data or a bunch of genes responsible for a function to be occurred. Irrespective to genes of any families, species, wild type or mutated, our paper here gives a standard model which defines a mapping between physicochemical properties of any arbitrary DNA sequence and physicochemical properties of its amino acid sequence. Experiments have been carried out with PPCA protein family and its four homologs PPC(B E) which establishes that DNA sequence keeps its signature even after its translation into the corresponding amino acid sequence.
Dynamic control of proinflammatory cytokines Il-1β and Tnf-α by macrophages is necessary for functional spinal cord regeneration in zebrafish
Authors: Tsarouchas Themistoklis M. , Wehner Daniel , Cavone Leonardo , Munir Tahimina , Keatinge Marcus , Lambertus Marvin , Underhill Anna , Barrett Thomas , Kassapis Elias , Ogryzko Nikolay , Feng Yi , van Ham Tjakko J. , Becker Thomas , Becker Catherina G. 
Published: May 2018

ABSTRACTSpinal cord injury leads to a massive response of innate immune cells (microglia, macrophages, neutrophils) both, in non-regenerating mammals and in successfully regenerating zebrafish, but the role of these immune cells in functional spinal cord regeneration in zebrafish has not been addressed. Here we show that inhibiting inflammation reduces and promoting it accelerates axonal regeneration in larval zebrafish. Mutant analyses show that peripheral macrophages, but not neutrophils or microglia, are necessary and sufficient for full regeneration. Macrophage-lessirf8mutants show prolonged inflammation with elevated levels of Il-1β and Tnf-α. Decreasing Il-1β levels or number of Il-1β+neutrophils rescues functional regeneration inirf8mutants. However, during early regeneration, interference with Il-1β function impairs regeneration inirf8and wildtype animals. Inhibiting Tnf-α does not rescue axonal growth inirf8mutants, but impairs it in wildtype animals, indicating a pro-regenerative role of Tnf-α. Hence, inflammation is tightly and dynamically controlled by macrophages to promote functional spinal cord regeneration in zebrafish.
Myosin-driven fragmentation of actin filaments triggers contraction of a disordered actin network
Authors: Matsuda Kyohei , Kobayashi Takuya , Sugawa Mitsuhiro , Koiso Yurika , Toyoshima Yoko Y. , Yajima Junichiro 
Published: May 2018

AbstractThe dynamic cytoskeletal network is responsible for cell shape changes and cell division. The actin-based motor protein myosin II drives the remodeling of a highly disordered actin-based network and enables the network to perform mechanical work such as contraction, migration and adhesion. Myosin II forms bipolar filaments that self-associate via their tail domains. Such myosin minifilaments generate both extensile and compressive forces that pull and push actin filaments, depending on the relative position of myosin and actin filaments in the network. However, it remains unclear how the mechanical properties of myosin II that rely on the energy of ATP hydrolysis spontaneously contract the disordered actin network. Here, we used a minimal in vitro reconstituted experimental system consisting of actin, myosin, and a cross-linking protein, to gain insights into the molecular mechanism by which myosin minifilaments organize disordered actin networks into contractile states. We found that contracted cluster size and time required for the onset of network contraction decreased as ATP concentration decreased. Contraction velocity was negatively correlated with ATP concentrations. Reduction of ATP concentration caused fragmentation of actin filaments by myosin minifilament. We also found that gelsolin, a Ca2+-regulated actin filament-severing protein, induced contraction of a mechanically stable network, implying that fragmentations of actin filaments in the network weaken the intra-network connectivity and trigger contraction. Our findings reveal that the disordered actin network contraction can be controlled by fragmentation of actin filaments, highlighting the molecular mechanism underlying the myosin motor-severing activities, other than the sliding tensile and compressive stress in the disordered actin network.
Focusing quorum sensing signalling by nano‐magnetic assembly
Authors: Guan Yongguang , Tsao Chen‐Yu , Quan David N. , Li Ying , Mei Lei , Song Yingying , Zhang Boce , Liu Yi , Payne Gregory F. , Bentley William E. , Wang Qin 
Published: May 2018

SummaryQuorum sensing (QS) exists widely among bacteria, enabling a transition to multicellular behaviour after bacterial populations reach a particular density. The coordination of multicellularity enables biotechnological application, dissolution of biofilms, coordination of virulence, and so forth. Here, a method to elicit and subsequently disperse multicellular behaviour among QS‐negative cells is developed using magnetic nanoparticle assembly. We fabricated magnetic nanoparticles (MNPs, ∼5 nm) that electrostatically collect wild‐type (WT) Escherichia coli BL21 cells and brings them into proximity of bioengineered E. coli [CT104 (W3110 lsrFG− luxS− pCT6 + pET‐DsRed)] reporter cells that exhibit a QS response after receiving autoinducer‐2 (AI‐2). By shortening the distance between WT and reporter cells (e.g., increasing local available AI‐2 concentrations), the QS response signalling was amplified four‐fold compared to that in native conditions without assembly. This study suggests potential applications in facilitating intercellular communication and modulating multicellular behaviours based on user‐specified designs.
Bloom of a denitrifying methanotroph, ‘Candidatus Methylomirabilis limnetica’, in a deep stratified lake
Authors: Graf Jon S. , Mayr Magdalena J. , Marchant Hannah K. , Tienken Daniela , Hach Philipp F. , Brand Andreas , Schubert Carsten J. , Kuypers Marcel M. M. , Milucka Jana 
Published: May 2018

SummaryMethanotrophic bacteria represent an important biological filter regulating methane emissions into the atmosphere. Planktonic methanotrophic communities in freshwater lakes are typically dominated by aerobic gamma‐proteobacteria, with a contribution from alpha‐proteobacterial methanotrophs and the NC10 bacteria. The NC10 clade encompasses methanotrophs related to ‘Candidatus Methylomirabilis oxyfera’, which oxidize methane using a unique pathway of denitrification that tentatively produces N2 and O2 from nitric oxide (NO). Here, we describe a new species of the NC10 clade, ‘Ca. Methylomirabilis limnetica’, which dominated the planktonic microbial community in the anoxic depths of the deep stratified Lake Zug in two consecutive years, comprising up to 27% of the total bacterial population. Gene transcripts assigned to ‘Ca. M. limnetica’ constituted up to one third of all metatranscriptomic sequences in situ. The reconstructed genome encoded a complete pathway for methane oxidation, and an incomplete denitrification pathway, including two putative nitric oxide dismutase genes. The genome of ‘Ca. M. limnetica’ exhibited features possibly related to genome streamlining (i.e. less redundancy of key metabolic genes) and adaptation to its planktonic habitat (i.e. gas vesicle genes). We speculate that ‘Ca. M. limnetica’ temporarily bloomed in the lake during non‐steady‐state conditions suggesting a niche for NC10 bacteria in the lacustrine methane and nitrogen cycle.
Political support among winners and losers: Within‐ and between‐country effects of structure, process and performance in Europe
Authors: MARTINI SERGIO , QUARANTA MARIO 
Published: May 2018

AbstractWhy is the winner‐loser gap in political support wider in some countries and narrower in others? Previous studies have focused on how the input side of political systems (i.e., the institutional structure) affects the winner‐loser gap. This study suggests that one should also consider the output side (i.e., the quality of political process and economic performance) and posits that two mechanisms – rational and psychological – can explain how output factors affect the gap. Going beyond previous research, this article also considers whether contextual characteristics explain the variation in the gap not only between countries, but also within them. Applying mixed models to survey data from 30 European countries between 2002 and 2015, the study finds that the differences in support between winners and losers across countries are smaller in consensual systems, as in these contexts the support among losers is higher. However, changes in the institutional structure do not explain the over‐time variation in the winner‐loser gap. Moreover, increasing quality of process and economic performance do not attenuate the gap across countries and over time, as they affect positively the political support of both winners and losers. The study shows which contextual factors explain the winner‐loser gap and points to the conditions that increase losers’ consent, which is a crucial element of democratic legitimacy.
Social stress shortens lifespan in mice
Authors: Razzoli Maria , Nyuyki‐Dufe Kewir , Gurney Allison , Erickson Connor , McCallum Jacob , Spielman Nicholas , Marzullo Marta , Patricelli Jessica , Kurata Morito , Pope Emily A. , Touma Chadi , Palme Rupert , Largaespada David A. , Allison David B. , Bartolomucci Alessandro 
Published: May 2018

SummaryStress and low socioeconomic status in humans confer increased vulnerability to morbidity and mortality. However, this association is not mechanistically understood nor has its causation been explored in animal models thus far. Recently, cellular senescence has been suggested as a potential mechanism linking lifelong stress to age‐related diseases and shorter life expectancy in humans. Here, we established a causal role for lifelong social stress on shortening lifespan and increasing the risk of cardiovascular disease in mice. Specifically, we developed a lifelong chronic psychosocial stress model in which male mouse aggressive behavior is used to study the impact of negative social confrontations on healthspan and lifespan. C57BL/6J mice identified through unbiased cluster analysis for receiving high while exhibiting low aggression, or identified as subordinate based on an ethologic criterion, had lower median and maximal lifespan, and developed earlier onset of several organ pathologies in the presence of a cellular senescence signature. Critically, subordinate mice developed spontaneous early‐stage atherosclerotic lesions of the aortic sinuses characterized by significant immune cells infiltration and sporadic rupture and calcification, none of which was found in dominant subjects. In conclusion, we present here the first rodent model to study and mechanistically dissect the impact of chronic stress on lifespan and disease of aging. These data highlight a conserved role for social stress and low social status on shortening lifespan and increasing the risk of cardiovascular disease in mammals and identify a potential mechanistic link for this complex phenomenon.
Probiotic supplementation improves reproductive performance of unvaccinated farmed sows infected with porcine epidemic diarrhea virus
Authors: Tsukahara Takamitsu , Inatomi Takio , Otomaru Konosuke , Amatatsu Masaaki , Romero‐Pérez Gustavo A. , Inoue Ryo 
Published: May 2018

AbstractWe investigated if probiotic supplementation could improve the health and reproductive performance of unvaccinated lactating sows infected with porcine epidemic diarrhea (PED) virus. Twenty unvaccinated pregnant sows were equally allocated to probiotic‐supplemented (P) and control (C) groups. For the experiment, 15 g/day of probiotic compound BIO‐THREE PZ was given to P sows. Reproductive performance was checked daily. The number of neonates fostered by each sow was maintained at eight throughout the experiment. Individual milk production post‐parturition was measured twice. Milk protein and fat ratios were determined by a milk analyzer. Total immunoglobulin (Ig) A and G concentrations were measured by ELISA. At day 7 post‐parturition, the body weight of P sows was 10 kg higher than that of C sows, and at day 3 post‐parturition, P sows produced more milk (+2 kg) and had a higher IgA concentration in whey than did C sows (p < .05). Finally, unlike C sows, P sows tended to return to estrus faster, and had larger piglets at birth with a lower mortality percentage during early days of suckling. In conclusion, probiotic compound BIO‐THREE PZ helped strengthen the immune system of unvaccinated, PED‐infected sows and improved their reproductive performance.
Symbolic play promotes non‐verbal communicative exchange in infant–caregiver dyads
Authors: Quinn Sara , Kidd Evan 
Published: May 2018

Symbolic play has long been considered a fertile context for communicative development (Bruner, 1983, Child's talk: Learning to use language, Oxford University Press, Oxford; Vygotsky, 1962, Thought and language, MIT Press, Cambridge, MA; Vygotsky, 1978, Mind in society: The development of higher psychological processes. Harvard University Press, Cambridge, MA). In the current study, we examined caregiver–infant interaction during symbolic play and compared it to interaction in a comparable but non‐symbolic context (i.e., ‘functional’ play). Fifty‐four (N = 54) caregivers and their 18‐month‐old infants were observed engaging in 20 min of play (symbolic, functional). Play interactions were coded and compared across play conditions for joint attention (JA) and gesture use. Compared with functional play, symbolic play was characterized by greater frequency and duration of JA and greater gesture use, particularly the use of iconic gestures with an object in hand. The results suggest that symbolic play provides a rich context for the exchange and negotiation of meaning, and thus may contribute to the development of important skills underlying communicative development.
Statement of contribution

Current knowledge

Symbolic play has long been linked to communicative development.

We do not know the extent to which the social context of symbolic play fosters communicative skills.

Present study

We test whether key communicative acts (joint attention, gesture) are more common in infant–caregiver dyads during symbolic versus functional play.

Joint attention was established more often and sustained for longer periods in symbolic play than in functional play.

Infants and caregivers produced more in‐hand representational gestures in symbolic compared to functional play.
Early to middle Holocene palaeoenvironmental reconstruction of the Beagle Channel (southernmost Argentina) based on terrestrial and marine palynomorphs
Authors: Candel María Soledad , Borromei Ana M. , Louwye Stephen 
Published: May 2018

This paper presents the main palaeoenvironmental results obtained from a site located in the western sector of the Beagle Channel, Isla Grande de Tierra del Fuego, southernmost Argentina. The palynological analysis performed on marine sediments from Aserradero‐Lapataia 2 (latitude 54°51′22.7″S, longitude 68°34′22.8″W) allowed us to document the evolution of palaeoenvironmental conditions during the beginning of the Holocene marine transgression into the Beagle Channel. The results indicate that, prior to the marine incursion, the coastal areas were characterized by the presence of open‐grown shrubs and herbs along with woodland palaeocommunities. The aquatic environments were dominated exclusively by freshwater taxa. Around 8300 cal. a BP, seawater gradually flooded the channel while cold and high effective moisture conditions favoured the development of an arboreal vegetation with dominance of Nothofagus forest and scarcity of shrub and herbaceous communities. Gradually increasing salinities allowed the development of freshwater/marine transitional environments indicated by aquatic palynomorphs able to tolerate stressed conditions under fluctuating salinities. The increasing dinocyst diversification with dominance of heterotrophic taxa corroborates the establishment of a fully marine environment during the middle–late Holocene in the Beagle Channel.
Approach or avoidance: Neural correlates of intelligence evaluation from faces
Authors: Akimoto Yoritaka , Yamazaki Ryuichi , Sugiura Motoaki , Nouchi Rui , Terao Chiaki , Tsukiura Takashi , Kawashima Ryuta 
Published: May 2018

AbstractIntelligence is among the key determinants of power and social status in modern societies. In this functional magnetic resonance imaging study, we examined the neural correlates of intelligence evaluation from faces. Participants underwent scans while they evaluated the perceived intelligence and friendliness of faces. We found that medial orbitofrontal cortex activity increased linearly with friendliness ratings. The relationship between perceived intelligence and brain activity was positively linear in the right caudate nucleus and U‐shaped (i.e., strong responses to unintelligent‐looking or intelligent‐looking faces) in the right anterior insula/inferior frontal gyrus. Perceived intelligence was also significantly positively correlated with both friendliness and attractiveness. Furthermore, intelligence rating scores had a positive linear effect on reaction times in the friendliness rating task, suggesting that participants had greater conflicts when making friendliness judgments for faces that appeared to belong to intelligent individuals. In addition, the degree of this effect predicted individual differences in the positive linear modulatory effect of intelligence scores in the right caudate nucleus. Our interpretation was that the activity in the caudate nucleus revealed an approach‐avoidance conflict with regard to highly intelligent people, that is, they were perceived as attractive but also potentially threatening. Although our interpretations are merely suggestive because we did not measure the approach‐avoidance behaviors directly, our findings have important implications for understanding the dynamics of human interaction in modern societies that increasingly allocate power and status based on intelligence.
Identification of two highly promiscuous thermostable sugar nucleotidylyltransferases for glycorandomization
Authors: Bais Vaibhav Singh , Batra Sahil , Prakash Balaji 
Published: May 2018

Glycorandomization is a process that improves the efficacy of glycoconjugates by the addition of a diverse array of sugars to secondary metabolites and antibiotics of pharmaceutical importance. This process, which employs sugar nucleotidylyltransferases (SNTs) and glycosyl transferases (GTs) in tandem, would benefit by the employment of promiscuous enzymes, i.e. those with the ability to utilize diverse noncanonical substrates. As promiscuous GTs are available, here we set out to identify promiscuous SNTs. For this, we began with a detailed family‐wide characterization of SNTs. Earlier, we had proposed that SNTs could be classified into two major groups – I and II. They share a common structural framework and utilize a similar catalytic mechanism. Subtle variations in the way two magnesium ions — and — are stabilized by metal ion coordination motifs led to their classification into diverse subgroups viz. I‐A, I‐B, I‐C, II‐A, and II‐B. Based on this classification, here we investigate promiscuity across the entire family of SNTs. We study the utilization of several sugar phosphates and nucleotides by the various subgroups of SNTs to understand substrate specificity and promiscuity in these. We find that promiscuity is prevalent among SNTs; and in particular, in the thermophilic homologs. In principle, promiscuity profiling identified four new SNTs that can be employed for the production of sugar‐nucleotide libraries. However, assaying for their ability to simultaneously utilize multiple substrates in a single‐pot reaction, we find two thermophilic SNTs‐ TMGA, an adenylyltransferase from Thermotoga maritima and PHGT, a thymidylyltransferase from Pyrococcus horikoshii that are readily employable for the production of diverse sugar‐nucleotides.
The second‐tier trap: Theory and experimental evidence
Authors: Kim Duk Gyoo 
Published: May 2018

AbstractWinner‐take‐all competitions can lead to the person in the second‐tier (middle‐tier) environment having the worst expected payoff when players exclusively choose their environment and exert effort before their random, heterogeneous environmental supports are realized. The tiers are defined by the ranks in pairwise competitions. The second‐tier trap (STT) is a situation in which a player from the second‐tier environment has the worst expected payoff even though his expected environmental support is strictly greater than that of the third‐tier player. A sufficient condition for the STT is that the ex‐ante advantages, the winning probabilities when all the players exert the same amount of effort regardless of their environment, are the same for those two environments. I claim that this sufficient condition for the STT is so weak that players can easily be tempted to choose the second‐tier environment, which is the wrong decision. Lab experiments strongly support this claim.
Different outdoor professions have different risks – a cross‐sectional study comparing non‐melanoma skin cancer risk among farmers, gardeners and mountain guides
Authors: Zink A. , Tizek L. , Schielein M. , Böhner A. , Biedermann T. , Wildner M. 
Published: May 2018

AbstractBackgroundOne of the main risk factors for non‐melanoma skin cancer (NMSC), the most common cancer worldwide, is solar ultraviolet radiation (UVR). This has led to the recognition of NMSC as occupational disease for outdoor workers in several countries. However, outdoor professions are a very heterogeneous group with diverse daily activities and associated UVR exposure.ObjectiveTo compare the prevalence of NMSC and associated risk behaviour in different outdoor professions.MethodsCross‐sectional study among outdoor workers (farmers, gardeners, mountain guides) and indoor workers (office employees) as control group using a paper‐based questionnaire on UVR exposure and protective behaviour followed by a skin examination by a dermatologist.ResultsA total of 563 participants (46.9% women, 46.9 ± 13.8 years) consisting of 348 outdoor workers (38.8% farmer, 35.3% gardener, 25.9% mountain guides) and 215 indoor workers were included in the study between March and September 2017. NMSC incl. actinic keratosis was diagnosed in 33.3% of mountain guides, 27.4% of farmers, 19.5% of gardeners and in 5.6% of indoor workers. Significant differences were seen between the outdoor professions with mountain guides at highest risk compared to farmers (OR = 2.6, 95% CI = 1.2–5.7). Substantial differences between the professions were also seen in skin cancer screening attendance rates (indoor worker 61.4%, mountain guides 57.8%, farmers 31.9%, gardeners 27.6%), daily UVR exposure during work and protective behaviour such as sunscreen use during work.ConclusionDifferent outdoor professions have significant different risks for NMSC and show different risk behaviour. Tailoring prevention efforts to different professions based on their individual needs could be the key to lower the global burden of (occupational) NMSC.