bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing functional and optical cross-sections of PSII in leaves during state transitions using fast repetition rate light induced fluorescence transients
Authors: Osmond Barry , Chow Wah Soon , Pogson Barry J. , Robinson Sharon A.
Published: March 2019

Plants adjust the relative sizes of PSII and PSI antennae in response to the spectral composition of weak light favouring either photosystem by processes known as state transitions (ST), attributed to a discrete antenna migration involving phosphorylation of light-harvesting chlorophyll-protein complexes in PSII. Here for the first time we monitored the extent and dynamics of ST in leaves from estimates of optical absorption cross-section (relative PSII antenna size; aPSII). These estimates were obtained from in situ measurements of functional absorption cross-section (σPSII) and maximum photochemical efficiency of PSII (φPSII); i.e. aPSII = σPSII/φPSII (Kolber et al. 1998) and other parameters from a light induced fluorescence transient (LIFT) device (Osmond et al. 2017). The fast repetition rate (FRR) QA flash protocol of this instrument monitors chlorophyll fluorescence yields with reduced QA irrespective of the redox state of plastoquinone (PQ), as well as during strong ~1 s white light pulses that fully reduce the PQ pool. Fitting this transient with the FRR model monitors kinetics of PSII → PQ, PQ → PSI, and the redox state of the PQ pool in the ‘PQ pool control loop’ that underpins ST, with a time resolution of a few seconds. All LIFT/FRR criteria confirmed the absence of ST in antenna mutant chlorina-f2 of barley and asLhcb2–12 of Arabidopsis, as well as STN7 kinase mutants stn7 and stn7/8. In contrast, wild-type barley and Arabidopsis genotypes Col, npq1, npq4, OEpsbs, pgr5 bkg and pgr5, showed normal ST. However, the extent of ST (and by implication the size of the phosphorylated LHCII pool participating in ST) deduced from changes in aʹPSII and other parameters with reduced QA range up to 35%. Estimates from strong WL pulses in the same assay were only ~10%. The larger estimates of ST from the QA flash are discussed in the context of contemporary dynamic structural models of ST involving formation and participation of PSII and PSI megacomplexes in an ‘energetically connected lake’ of phosphorylated LHCII trimers (Grieco et al. 2015). Despite the absence of ST, asLhcb2-12 displays normal wild-type modulation of electron transport rate (ETR) and the PQ pool during ST assays, reflecting compensatory changes in antenna LHCIIs in this genotype. Impaired LHCII phosphorylation in stn7 and stn7/8 accelerates ETR from PSII →PQ, over-reducing the PQ pool and abolishing the yield difference between the QA flash and WL pulse, with implications for photochemical and thermal phases of the O-J-I-P transient.
The Moyjil site, south-west Victoria, Australia: fire and environment in a 120,000-year coastal midden — nature or people?
Authors: Bowler Jim M. , Price David M. , Sherwood John E. , Carey Stephen P.
Published: March 2019

At Moyjil (Point Ritchie), a cliffed site at the mouth of the Hopkins River at Warrnambool, south-eastern Australia, an erosional disconformity of Last Interglacial age on both a rock stack and the adjacent headland represents a surface of possible human occupation. Shells of edible marine molluscs occur on the disconformity, together with a distinctive population of transported stones derived from a calcrete of MIS 7 age and bearing variable dark grey to near-black colouration suggestive of fire. Experimental fire produced similar thermal alteration of calcrete. A strong correlation exists between intensity and depth of dark staining on one hand and increased magnetic susceptibility on the other. Thermal luminescence analyses of blackened stones provide ages in the MIS 5e range, 100–130 ka, consistent with independent stratigraphic evidence and contemporaneous with the age of the surface on which they lie. The distribution of fire-darkened stones is inconsistent with wildfire effects. Two hearth-like features closely associated with the disconformity provide further indications of potential human agency. The data are consistent with the suggestion of human presence at Warrnambool during the Last Interglacial.
The Moyjil site, south-west Victoria, Australia: excavation of a Last Interglacial charcoal and and burnt stone feature — is it a hearth?
Authors: McNiven Ian J. , Crouch Joe , Bowler Jim M. , Sherwood John E. , Dolby Nic , Dunn Julian E. , Stanisic John
Published: March 2019

Claims for a human presence in Australia beyond 60,000 years ago must have a strong evidence base associated with rigorous methodology and intense scrutiny. In this light we present excavation results for Charcoal and Burnt Stone Feature #1 (CBS1) located within coastal dune sediments at Moyjil (Point Ritchie), Warrnambool, that independent geomorphic and OSL dating indicates is of Last Interglacial age (~120,000 years ago). While on plausibility grounds the cultural status of a feature of such great antiquity in Australia is unlikely, a cultural origin for CBS1 is less easily dismissed if assessed with an age-independent methodology. A broad range of macroscale discrimination criteria has been used to assess whether CBS1 is either a cultural hearth or a natural feature such as a burnt tree stump. On balance, evidence marginally supports a cultural origin over a natural origin. However, the absence of associated stone artefacts and faunal remains and the presence of burnt root wood precludes definitive statements on the cultural status of the feature. Our case study is methodologically instructivein terms of the potential complexities and issues of equifinality involved in the archaeological identification of ancient hearths.
Resistance of Pinus pinea L. bark to fire
Authors: Madrigal Javier , Souto-García Jennifer , Calama Rafael , Guijarro Mercedes , Picos Juan , Hernando Carmen
Published: March 2019

The stone pine (Pinus pinea L.) has thick bark as an adaptation to wildfire. In this study, laboratory tests were carried out to quantify the influence of bark thickness on flammability and fire resistance in this species. Heating rate in the cambium and the time to reach lethal temperatures in living tissues were determined using a mass loss calorimeter. In addition, data from permanent plots were used to generate linear mixed models to predict bark thickness along the trunk in stone pine stands. The combination of laboratory and field data provided information about the critical threshold of bark thickness (2cm) below which the heat transmission rate would increase, decreasing the time to reach lethal temperatures in the cambium and therefore the resistance to fire. A new model was developed to calculate critical thresholds of charring height that guarantee efficient protection from fire along the trunk. Predicting whether the bark is thick enough to help trees survive may have important applications in the field of forest fuel management and in the ecology of these pine forests, as well as in preventive silviculture to assess critical heights of trunks likely to be affected during wildfire and prescribed burning.
Research interviewers as ‘knowers’ and ‘unknowers’
Authors: Roulston Kathryn
Published: March 2019

The qualitative research interview is ubiquitously framed as producing information about research participants’ beliefs, perspectives, opinions and experiences. These beliefs, perspectives, opinions and experiences are derived from people who are experts on their selves – that is, they have first-person knowledge of the “territories of the self” (Goffman 1971
). In concert with Goffman’s work on territories of the self, in this chapter I use work on epistemics in conversation as a tool to explore how interviewers elicit knowledge claims from research participants during interviews. Scholarship on interviewing describes the dilemma faced by research interviewers who must navigate the spectrum of potential relationships with interviewees: on the one hand, as an “insider” to a culture, “everything goes without saying”; at the other extreme, “total divergence” in which interviewer and interviewee have no shared language with which to speak about topics (
Bourdieu et al. 1999). Yet, between these two poles lie any number of potential stances from which more or less knowledgeable (K+/K−) interviewers ask questions seeking information from more or less knowledgeable (K+/K−) (Heritage 2013) research participants. This chapter examines excerpts from interview data to explore key ideas drawn from literature on epistemics in conversation analysis to consider the researcher’s work of asking questions in research interviews for the purpose of knowledge production.
On doing ‘being feminist’ and ‘being researcher’
Authors: Herron Brigette Adair
Published: March 2019

Novice interviewers can face many problems related to interviewing technique, theoretical and ethical tensions, developing rapport, and the production of knowledge and identities with strangers and in cross-cultural contexts. Reanalyzing problematic or failed interviews using ethnomethodological (EM) approaches and the tools of membership categorization analysis (MCA) is one way of exploring minute details of interview talk to improve interview conduct. Using an EM approach and the tools of MCA, this chapter re-examines previously abandoned interview data to demonstrate how conversational resources used by a novice interviewer and interviewee led to the production of shared understandings and the production of various identities in cross-cultural contexts. This chapter concludes with recommendations for using this kind of analysis when training novice interviewers. This work recommends an intentional approach to thinking through researcher ethics before interviews are conducted to promote interview practices where data are generated, analyzed, and represented in more ethical ways.
“What does it mean?”
Authors: Smith Rebecca Ann
Published: March 2019

Social, cultural, and institutional norms invoked by adults in school settings often limit children’s voices in educational research. This chapter re-examines interview data, focusing on methodologies used to address the challenges associated with interviewing children. For this analysis, three challenges have been identified from transcripts: limiting the child/adult binary, analyzing children’s language, and overcoming children’s inexperience with interviewing. To address these challenges, this chapter focuses on methodological strategies used in an ethnographically inspired research study. These strategies included framing children’s positions through the reconceptualized model of childhood, using open or emergent listening (Davies 2011, 2014) during interviews, and reactive entry methods (Corsaro 1985, 2003). The analysis of the children’s language is expanded to include the bodily ways or multimodal forms of communication and the closer examination of the children’s abilities to participate in multiple conversations during interviews. Excerpts from interviews initially perceived to have “failed” are examined to understand how children’s inexperience with interviewing can be misinterpreted as unpredictable. Finally, interviews are interpreted as pedagogical encounters in which children are taught cultural and social norms.
“But you’re gonna ask me questions, right?”
Authors: Veronesi Daniela
Published: March 2019

By adopting a “social practice” perspective of qualitative interviews, and thereby considering such tool of data collection as a joint accomplishment of both interviewee and interviewer, in this chapter the author examines language biography interviews as they are co-constructed by conversational partners. Using conversation analysis (CA), the chapter looks at how participants locally negotiate the interactional frame of their encounter as institutional talk leading to the generation of research data. How interviewees display their “for the record” orientation by assessing their own talk, as well by drawing upon the encounter as a resource to let their voice be heard is then discussed.
The way(s) of interviewing
Authors: Rapley Tim
Published: March 2019

In this closing chapter, I will offer some thoughts about how this volume extends existing methodological literature on qualitative interviewing, as well as further ideas for exploration. I will show how this volume offers a future direction for a range of work, including a focus on different modes or forms of interviews, identities and epistemics, as well as the role of the interview schedule. Finally, I show that despite this volume’s focus on the interactional work within interview interactions, it also suggests a trajectory of work that looks both across and beyond the spaces of the interview interactions.
Effects of temperature and strain rate in strain hardening in torsion of a twinning-induced plasticity steel
Authors: de las Cuevas Fernando , Gil Sevillano Javier
Published: March 2019

A series of torsion tests were performed to characterise the plastic response at high strain levels in a twinning-induced plasticity steel (22%Mn–0.6%C in mass) in the interval of temperatures 20°C ≤  T ≤ 450°C at three different shear strain rates, [Formula: see text], 2.4·10−3, 0.2, 6.5 s−1. The work hardening at room temperature was near-linear typical of this steel. It was found that the work hardening rate and the torsional ductility are strongly influenced by temperatures T ≥ 150°C. Sub-surface deformed specimens at T = 450°C and 2.4·10−3 s−1 were analysed via high-resolution electron backscatter diffraction system, showed a sub-structure of very fine grains indicating that continuous dynamic recrystallization had taken place.
Time-evolution of microstructure and mechanical behaviour of double annealed medium Mn steel
Authors: Arlazarov Artem , Goune Mohamed , Bouaziz Olivier , Kegel Frédéric , Hazotte Alain
Published: March 2019

Cold rolled 0.1C-4.7Mn (wt-%) steel was submitted to double annealing. The holding time of second intercritical annealing at 650°C was varied between 3 min and 30 h. Tensile behavior after each treatment was measured and analysed. Microstructure characterisation was performed using field emission gun scanning electron microscope, transmission electron microscope and saturation magnetisation method. Moreover, interrupted tensile tests were done to obtain the kinetics of austenite destabilisation during straining. An important effect of soaking time on the microstructure and associate mechanical properties was revealed and analysed. Considering thermal and mechanical stability of retained austenite, the optimum combination of phases, providing the best strength-ductility balance, was found after 2 h holding.

This paper is part of a Thematic Issue on Medium Manganese Steels.
Induction of neutralizing antibodies by human papillomavirus vaccine generated in mammalian cells
Authors: Wu Xilin , Ma Xiaohua , Li Yanlei , Xu Yue , Zheng Nan , Xu Shijie , Nawaz Waqas , Wu Zhiwei
Published: March 2019

Background

Cervical cancer caused by human papillomavirus (HPV) infections is one of the most common cancers affecting women worldwide. Current preventative HPV vaccines on the market are composed of HPV L1 protein produced either in the yeast such as Gardasil or in the insect cells such as Cervarix. The duration of efficacy and cross-protection remain highly desirable for the improvement of current prophylactic HPV vaccine. Given that HPV carries out infection and replicates in mammalian cells, L2 protein, which is not included in the current licensed vaccines, is included in the third generation of HPV vaccine in pursuing of providing broader prevention. We hypothesize that a virus-like particle (VLP) consisting of HPV L1 plus L2 proteins generated in mammalian cells will present conformations more closely to native HPV, thus it will provide more durable and broader efficacy of prevention.

Methods

We took advantage of 293TT cells to produce VLP containing L1 and L2 proteins of HPV16 and HPV18, respectively.

Results

VLP particles of uniformed size and morphology were observed, and potent and broadly neutralizing antibodies were induced in mice and rabbits. In addition, compared to bivalent HPV vaccine of Cervarix, our HPV L1-L2 VLPs elicited higher titer of anti-sera, and the anti-sera also presented comparable neutralization potency against HPV16 and HPV18 infections even a much less potent adjuvant was used in our case.

Conclusion

Our VLPs were capable of eliciting stronger and more broadly neutralizing activities against various HPV subtypes and were potential candidate HPV vaccines.
The Ends of Human Rights in US Literary Studies
Authors: Goodman Brian K
Published: March 2019

How has contemporary US literature responded to the rapid rise and subsequent decline of human rights in US political discourse? In this essay-review, I examine two recent works—James Dawes’s The Novel of Human Rights (2018) and Crystal Parikh’s Writing Human Rights (2017)—that each bring a critical human rights approach to the study of contemporary US literatures. The essay begins by describing the emergence of the subfield of literature and human rights and its original investment in methodologies of ideology critique. I then show how Dawes and Parikh each adopt a dialectical method to investigate the contradictory relationship between a subset of contemporary American novels and a US-centric, liberal conception of human rights, while also mapping the emergence of new generic forms. But can new kinds of stories transform human rights in practice? To address this question, the essay next examines the role of literature in recent historiographic debates about the origins of human rights in order to argue for a literary-historical turn in the subfield of literature and human rights. Calling for new work that grounds the subfield’s ongoing critique of human rights representations in specific historical practices of the human rights, I conclude by briefly considering Toni Morrison’s novel Beloved (1987) alongside her involvement with the human rights movement. Can a search for literary precursors help us imagine a different future for human rights?
Microbial Colonization in Adulthood Shapes the Intestinal Macrophage Compartment
Authors: Schmidt Franziska , Dahlke Katja , Batra Arvind , Keye Jacqueline , Wu Hao , Friedrich Marie , Glauben Rainer , Ring Christiane , Loh Gunnar , Schaubeck Monika , Hackl Hubert , Trajanoski Zlatko , Schumann Michael , Kühl Anja A , Blaut Michael , Siegmund Britta
Published: March 2019

Background and Aims

Contact with distinct microbiota early in life has been shown to educate the mucosal immune system, hence providing protection against immune-mediated diseases. However, the impact of early versus late colonization with regard to the development of the intestinal macrophage compartment has not been studied so far.

Methods

Germ-free mice were colonized with specific-pathogen-free [SPF] microbiota at the age of 5 weeks. The ileal and colonic macrophage compartment were analysed by immunohistochemistry, flow cytometry, and RNA sequencing 1 and 5 weeks after colonization and in age-matched SPF mice, which had had contact with microbiota since birth. To evaluate the functional differences, dextran sulfate sodium [DSS]-induced colitis was induced, and barrier function analyses were undertaken.

Results

Germ-free mice were characterized by an atrophied intestinal wall and a profoundly reduced number of ileal macrophages. Strikingly, morphological restoration of the intestine occurred within the first week after colonization. In contrast, ileal macrophages required 5 weeks for complete restoration, whereas colonic macrophages were numerically unaffected. However, following DSS exposure, the presence of microbiota was a prerequisite for colonic macrophage infiltration. One week after colonization, mild colonic inflammation was observed, paralleled by a reduced inflammatory response after DSS treatment, in comparison with SPF mice. This attenuated inflammation was paralleled by a lack of TNFα production of LPS-stimulated colonic macrophages from SPF and colonized mice, suggesting desensitization of colonized mice by the colonization itself.

Conclusions

This study provides the first data indicating that after colonization of adult mice, the numeric, phenotypic, and functional restoration of the macrophage compartment requires the presence of intestinal microbiota and is time dependent.
Impact of preservation of the latissimus dorsi muscle through a left anteroaxillary thoracotomy on spinal cord protection in descending thoracic and thoraco-abdominal aortic operations†
Authors: Fujiyoshi Toshiki , Nishibe Toshiya , Koizumi Nobusato , Kano Masaki , Suzuki Shun , Iwahori Akinari , Maruno Keta , Kawago Koji , Takahashi Satoshi , Iwahashi Toru , Kamiya Kentarou , Ogino Hitoshi
Published: March 2019

OBJECTIVES

The presence of collateral network circulation to the spinal cord, which is reflected in the repair of a descending thoracic aortic aneurysm (dAo) and a thoraco-abdominal aortic aneurysm (TAAo), has been demonstrated in clinical and animal experimental data. The latissimus dorsi muscle (LDM) including the thoracodorsal artery might be one of the major sources of this collateral network. The objective of this study was to evaluate the impact on spinal cord safety of a left anteroaxillary thoracotomy with minimal muscle division including preservation of the LDM in surgery for dAo and TAAo.

METHODS

Sixty-nine patients [64 (23–85) years old; 56 men] who underwent surgical repair for dAo and TAAo were divided into 2 groups: 29 [65 (23–84) years old] with an anteroaxillary thoracotomy with LDM preservation (PL group) and 40 [61 (28–85) years old] with a lateral thoracotomy without LDM preservation (NL group).

RESULTS

Aortic repairs were performed at the dAo in 30 patients including 14 in the PL group vs 16 in the NL group and at the TAAo in 39 patients including 15 in the PL group vs 24 in the NL group. There were 2 (2.9%) 30-day deaths; 2 (7.9%) in the PL group vs none in the NL group (P = 0.173). No strokes occurred. In patients with a femoro-femoral partial cardiopulmonary bypass with mild hypothermia, the incidence of loss of signal of motor-evoked potentials (>50%) was significantly lower in the PL group; 5.6% vs 31.8% (P = 0.039). The frequency of signal reduction of the remaining motor-evoked potential after surgery was also significantly lower in the PL group: 3.7% vs 25% (P = 0.040). Subsequently, the rate of spinal cord complications were lower in the PL group: 3.4% vs 12.5% (P = 0.188).

CONCLUSIONS

The left anteroaxillary thoracotomy with minimal incision of the muscles including the LDM might have potential advantages for spinal cord protection via preserved intramuscular collateral circulations to the spinal cord in dAo/TAAo open repairs.
The Role of Departure States in Combating Irregular Emigration in International Law: An Historical Perspective
Authors: Wolman Andrew
Published: March 2019

This article examines the evolution over time of attempts to establish an international law principle that States have a legal responsibility, at least under certain circumstances, to combat irregular emigration, defined as the exit of individuals who would be arriving at their destination in a manner that is not compliant with the destination country’s immigration laws. Through examination of contemporaneous statements and the travaux préparatoires relating to six separate negotiations, light is shed on the attempts to develop such a norm since the beginning of the 20th century, along with the evolving set of legal and ethical justifications that were used in these processes. The different practical and principled objections employed by States and civil society actors to oppose the development of such a legal norm are also examined. The article concludes that this historical perspective challenges current perceptions that home State controls are of recent origin, and that in fact international migration law is inherently progressive.
Azole resistance and cyp51A mutation screening in Aspergillus fumigatus in Mexico
Authors: Gonzalez-Lara Maria F , Roman-Montes Carla M , Diaz-Lomeli Paulette , Rangel-Cordero Andrea , Valenzuela Maria O , Ponce-de-Leon Alfredo , Sifuentes-Osornio Jose , Ostrosky-Zeichner Luis , Martinez-Gamboa Areli
Published: March 2019

Background

Fungicide exposure in the environment has driven the emergence of azole-resistant Aspergillus fumigatus worldwide. A screening test allows identification of resistant isolates.

Objectives

We screened clinical samples for azole-resistant Aspergillus through azole-containing agar plates and identified mutations in the cyp51A gene of A. fumigatus.

Methods

Aspergillus isolates from clinical samples collected in a tertiary care centre from 2014 to 2017 were screened for azole resistance. Samples were subcultured in azole-containing agar plates. Isolates with a positive screening test were subject to DNA extraction, DNA amplification and sequencing of the cyp51A gene (coding and promoter regions). Clinical data were obtained from medical records.

Results

We screened 43 Aspergillus isolates from 39 patients for azole resistance. Three isolates from three patients grew on azole-containing agar plates: two A. fumigatus and one Aspergillus flavus. PCR analysis and cyp51A sequencing identified the TR34/L98H mutation in both A. fumigatus isolates. The prevalence of cyp51A mutations among A. fumigatus was 8.3% (2/24). Both patients with TR34/L98H mutants were azole naive and presented with invasive aspergillosis; one had multiple myeloma and the other was a liver retransplant recipient. They suffered progressive disease and failed voriconazole therapy.

Conclusions

To the best of our knowledge, this is the first report of azole-resistant A. fumigatus with the TR34/L98H mutation in two azole-naive patients with refractory invasive aspergillosis in Mexico.
Use of intensity-modulated radiation therapy for nasopharyngeal cancer in Japan: analysis using a national database
Authors: Rikitake Ryoko , Tsukada Yoichiro , Ando Mizuo , Yoshida Masafumi , Iwamoto Momoko , Yamasoba Tatsuya , Higashi Takahiro
Published: March 2019

Background

Intensity-modulated radiation therapy (IMRT) yields better outcomes and fewer toxicities for radiation therapy (RT) of head and neck cancers (HNCs), including nasopharyngeal cancer (NPC). IMRT is the standard RT treatment and has been widely adopted in Western countries to treat HNCs. However, its uptake in clinical practice among NPC patients has never been studied.

Methods

We investigated the use of IMRT for NPC using data from a nationwide cancer registry to describe the use of IMRT among NPC patients in Japan. We analyzed the data of patients with HNC, including NPC, who underwent IMRT between 2012 and 2014, as recorded in the hospital-based cancer registries linked with insurance claims. We calculated the proportion of patients with NPC who underwent IMRT at each hospital. To evaluate the use of IMRT for NPC, the IMRT use for NPC was compared with the proportion of patients with prostate cancer who underwent IMRT.

Results

Among 508 patients with NPC who underwent RT at one of 87 hospitals, 348 (69%) underwent IMRT. This proportion gradually increased between 2012 and 2014 (62%, 64% and 77%). Meanwhile, 4790 patients with prostate cancer (90%) underwent IMRT. Although some hospitals where IMRT was performed treated many patients with NPC, the proportion of patients with NPC who were treated with IMRT was low.

Conclusions

IMRT has not been widely adopted in Japan for treating NPC. Barriers for adopting its use should be identified to close the gap between the standard and actual medical practice in Japan.
Nematotoxicity of Paeonia spp. Extracts and Camellia oleifera Tea Seed Cake and Extracts to Heterodera glycines and Meloidogyne incognita
Authors: Wen Yanhua , Meyer Susan L. F. , MacDonald Margaret H. , Zheng Liuchun , Jing Chunyue , Chitwood David J.
Published: March 2019

Tea-oil camellia (Camellia oleifera) is grown for tea seed oil production, with tea seed cake produced as a byproduct. Rather than disposing of the cake, agricultural uses increase the value of oil production. Constituents of C. oleifera are also utilized for traditional Chinese medicine, as are compounds produced by tree peony roots. Consequently, the unused C. oleifera cake, and stems from two tree peony species, Paeonia rockii and Paeonia suffruticosa, were studied for compounds antagonistic to soybean cyst nematode (Heterodera glycines) and root-knot nematode (Meloidogyne incognita). Extracts from C. oleifera cake and P. rockii stems suppressed hatch and were nematotoxic to second-stage juveniles (J2) of both nematode species. P. rockii extracts were more effective than P. suffruticosa extracts for decreasing M. incognita hatch and J2 viability. In greenhouse trials with soybean (Glycine max ‘Essex’), powdered C. oleifera cake applied as a soil amendment suppressed H. glycines cysts/g root by up to 66% compared with nonamended controls. These results indicate that the extracts and cake contain compounds active against H. glycines and M. incognita, with activity varying between the two Paeonia species. C. oleifera tea seed cake, and constituents of the cake or of P. rockii, are candidates for further studies on management of these nematodes.
Systematic Identification of Pathogenic Streptomyces sp. AMCC400023 That Causes Common Scab and Genomic Analysis of Its Pathogenicity Island
Authors: Liang Feiyang , Lin Rongshan , Yao Yaqian , Xiao Yunli , Zhang Mingshuo , Shi Chunyu , He Xiaoli , Zhou Bo , Wang Bing
Published: March 2019

Potato scab, a serious soilborne disease caused by Streptomyces spp., occurs in potato-growing areas worldwide and results in severe economic losses. In this paper, the pathogenicity of Streptomyces strain AMCC400023, isolated from potato scabs in Hebei Province, China, was verified systematically by the radish seedling test, the potato tuber slice assay, the potted back experiment, and the detection of phytotoxin thaxtomin A. Morphological, physiological, and biochemical characteristics were determined, and the 16S ribosomal RNA analyses of Streptomyces sp. AMCC400023 were carried out. To obtain the accurate taxonomic status of the pathogen strain, the whole genome was sequenced, and the phylogenetic tree among 31 Streptomyces genomes was formed. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) were analyzed, and at the same time, the toxicity-related genes between Streptomyces sp. AMCC400023 and Streptomyces scabiei were compared, all based on the whole-genome level. All of the data supported that, instead of a member of S. scabiei, test strain Streptomyces sp. AMCC400023 was a distinct phytopathogen of potato common scab, which had a relatively close relationship with S. scabiei while separating clearly from S. scabiei at least in the species level of taxonomic status. The complete pathogenicity island (PAI) composition of Streptomyces sp. AMCC400023 was identified, which contained a toxin region and a colonization region. It was conjectured that the PAI of Streptomyces sp. AMCC400023 might be directly or indirectly acquired from S. scabiei 87-22 by horizontal gene transfer, or at the very least, there was a very close homologous relationship between the two pathogens as indicated by a series of analyses, such as phylogenetic relationships among 31 Streptomyces species, ANI and isDDH analyses, PAI structure mapping, thaxtomin A synthetic gene cluster tree construction, and most important, the collinearity analysis at the genome level.
Histological and Gene Expression Analyses in Banana Reveals the Pathogenic Differences between Races 1 and 4 of Banana Fusarium Wilt Pathogen
Authors: Dong Honghong , Fan Huiyun , Lei Zhaoxi , Wu Chao , Zhou Dengbo , Li Huaping
Published: March 2019

Fusarium oxysporum f. sp. cubense, the causative agent of Panama disease, is classified into three races: Foc1, Foc2, and Foc4. However, the histological characteristics, the accumulation of fusaric acid (FA), and resistant gene expression in banana infected with different races remain unclear. In this study, we compared the infection processes, FA contents, and gene expression levels in a Cavendish banana cultivar (Musa AAA Brazilian) inoculated with Foc1 and Foc4. Results showed that Foc4 can rapidly extend from the roots to the leaves, whereas Foc1 expands slowly from the roots to the rhizomes but cannot expand further upward. In addition, the colonization of plants by Foc4 was significantly higher compared with Foc1, as was the content of FA in those infected plant tissues. We observed that a large amount of starch granules was produced in the rhizomes and the number of starch granules was significantly higher after infection with Foc1 than after infection with Foc4. We further found that starch has an important inhibitory effect on the phytotoxicity induced by FA, thus leading to more resistance to the pathogens in the plants with high amounts of starch accumulation than in those with a low amount of starch accumulation. Moreover, the expression levels of 10 defense-related genes were analyzed and the results showed that the induction levels of those genes were higher after infection with Foc1 than after infection with Foc4. These results suggest that the observed differences in the invasion of host tissues and FA accumulation, and the number of starch granules and expression of defense-related genes, may contribute to a difference in virulence between the two races and the resulting difference in host resistance response, respectively.
Thermodynamics of rapid solidification and crystal growth kinetics in glass-forming alloys
Authors: Galenko P. K. , Ankudinov V. , Reuther K. , Rettenmayr M. , Salhoumi A. , Kharanzhevskiy E. V.
Published: March 2019

Thermodynamic driving forces and growth rates in rapid solidification are analysed. Taking into account the relaxation time of the solute diffusion flux in the model equations, the present theory uses, in a first case, the deviation from local chemical equilibrium, and ergodicity breaking. The second case of ergodicity breaking may exist in crystal growth kinetics of rapidly solidifying glass-forming metals and alloys. In this case, a theoretical analysis of dendritic solidification is given for congruently melting alloys in which chemical segregation does not occur. Within this theory, a deviation from thermodynamic equilibrium is introduced for high undercoolings via gradient flow relaxation of the phase field. A comparison of the present derivations with previously verified theoretical predictions and experimental data is given.

This article is part of the theme issue ‘Heterogeneous materials: metastable and non- ergodic internal structures’.
Liquid phase separation in undercooled Cu–Co alloys under the influence of static magnetic fields
Authors: Zhao Dandan , Gao Jianrong
Published: March 2019

Undercooling of Cu-based alloys often induces metastable liquid phase separation followed by rapid solidification of separated liquids. The rapid solidification can help freeze in the morphology of a higher-melting liquid and eases difficulties in studies of liquid phase separation kinetics. In the present work, the influence of static magnetic fields on liquid phase separation in bulk Cu
84
Co
16
composition was investigated. Inductively melted samples were glass-fluxed, undercooled and solidified under uniform and non-uniform magnetic fields generated by a superconducting magnet. Solidification microstructure of the phase-separated samples was examined using an optical microscope. The imposition of the magnetic fields, both uniform and non-uniform, altered the morphology, segregation pattern and size distribution of Co-rich droplets due to liquid phase separation. The imposition of the non-uniform magnetic fields with positive and negative gradients brought about segregation of the Co-rich droplets at the top and the bottom side of the samples, respectively. Such influence of the static magnetic fields is interpreted by assuming intensification of convective flow and Kelvin force-controlled migration of the Co-rich droplets.

This article is part of the theme issue ‘Heterogeneous materials: metastable and non-ergodic internal structures’.
Mechanical properties of magnetic gels containing rod-like composite particles
Authors: Abrougui Mariem M. , Lopez-Lopez Modesto T. , Duran Juan D. G.
Published: March 2019

Magnetic gels (ferrogels) are heterogeneous systems structured at the nanoscale that contains magnetic particles dispersed in three-dimensional networks of polymer chains. In the present work, the magnetic particles were synthesized with a core–shell structure, consisting of sepiolite particles covered by magnetite nanoparticles. These composite particles had a rod-like shape with a high aspect ratio. The obtained sepiolite–magnetite particles showed a high enough susceptibility and saturation magnetization. The magneto-rheological (MR) properties, and the intensity of the MR effect, of aqueous suspensions of the synthesized particles were studied. The particles, functionalized by adsorption of alginate molecules, were imbedded in alginate hydrogels to get homogeneous soft materials. The particles were linked to the polymer chains as the knots in a network and dominated in a great extent the mechanical properties of the materials. After determining the optimal compositions of the ferrogels, their viscoelastic properties were measured in the absence/presence of magnetic fields. The results pointed out that the MR effect provided by the clay–magnetite particles was considerably more intense than those achieved in ferrogels that contain spherical magnetic microparticles. Therefore, the imbedding of rod-shaped magnetic particles in hydrogels allows controlling the mechanical properties in a wider range than in conventional ferrogels.

This article is part of the theme issue ‘Heterogeneous materials: metastable and non-ergodic internal structures’.
Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1
Authors: Poganik Jesse R. , Long Marcus J. C. , Disare Michael T. , Liu Xuyu , Chang Sung-Hee , Hla Timothy , Aye Yimon
Published: March 2019

The Nrf2-driven antioxidant response (AR) is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of AR has centered on protein-level regulation of Nrf2. Here we report a post-transcriptional modality to directly regulate Nrf2-mRNA. Our initial studies focused on the effects of the key mRNA-binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These data led us to discover a novel role of HuR in regulating Nrf2/AR, and in the process we further identified the related mRBP AUF1 as an additional novel Nrf2/AR regulator. Both mRBPs regulate AR by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2-mRNA maturation and promotes its nuclear export; whereas AUF1 stabilizes Nrf2-mRNA. Both mRBPs target the 3′–UTR of Nrf2-mRNA. Using an AR-reporter zebrafish strain, we document that this post-transcriptional control of AR is conserved at the whole-vertebrate level.
Constraint-based analysis for causal discovery in population-based biobanks
Authors: Amar David , Ashley Euan , Rivas Manuel A.
Published: March 2019

Availability of large genetic databases has led to the development of powerful causal inference methods that use genetic variables as instruments to estimate causal effects. Such methods typically make many assumptions about the underlying causal graphical model, are limited in the patterns they search for in the data, and there is no guide for systematic analysis of a large database. Here, we present cGAUGE, a new pipeline for causal Graphical Analysis Using GEnetics that utilizes large changes in the significance of local conditional independencies between the genetic instruments and the phenotypes. We detect cases where causal inference can be performed with minimal risk of horizontal pleiotropy. Moreover, we search for new graphical patterns to reveal novel information about the underlying causal diagram that is not covered by extant methods, including new direct links, colliders, and evidence for confounding. We present theoretical justification, simulations, and apply our pipeline to 70 complex phenotypes from 337,198 subjects from the UK Biobank. Our results cover 102 detected causal relationships, of which some are new and many are expected. For example, we detect a direct causal link from high cholesterol to angina and a feedback loop between angina and myocardial infarction. We also corroborate a recent observational link between asthma and Crohn’s disease. Finally, we detect important features of the causal network structure including several causal hubs such as intelligence and waist circumference.
EpiAlign: an alignment-based bioinformatic tool for comparing chromatin state sequences
Authors: Ge Xinzhou , Zhang Haowen , Xie Lingjue , Li Wei Vivian , Kwon Soo Bin , Li Jingyi Jessica
Published: March 2019

The availability of genome-wide epigenomic datasets enables in-depth studies of epigenetic modifications and their relationships with chromatin structures and gene expression. Various alignment tools have been developed to align nucleotide or protein sequences in order to identify structurally similar regions. However, there are currently no alignment methods specifically designed for comparing multi-track epigenomic signals and detecting common patterns that may explain functional or evolutionary similarities. We propose a new local alignment algorithm, EpiAlign, designed to compare chromatin state sequences learned from multi-track epigenomic signals and to identify locally aligned chromatin regions. EpiAlign is a dynamic programming algorithm that novelly incorporates varying lengths and frequencies of chromatin states. We demonstrate the effcacy of EpiAlign through extensive simulations and studies on the real data from the NIH Roadmap Epigenomics project. EpiAlign is able to extract recurrent chromatin state patterns along a single epigenome, and many of these patterns carry cell-type-specific characteristics. EpiAlign can also detect common chromatin state patterns across multiple epigenomes, and it will serve as a useful tool to group and distinguish epigenomic samples based on genome-wide or local chromatin state patterns.
Contribution of Apical and Basal Dendrites of L2/3 Pyramidal Neurons to Orientation Encoding in Mouse V1
Authors: Park Jiyoung , Papoutsi Athanasia , Ash Ryan T. , Marin Miguel A. , Poirazi Panayiota , Smirnakis Stelios M.
Published: March 2019

Pyramidal neurons integrate synaptic inputs from basal and apical dendrites to generate stimulus-specific responses. It has been proposed that feed-forward inputs to basal dendrites drive a neuron’s stimulus preference, while feedback inputs to apical dendrites sharpen selectivity. However, how a neuron’s dendritic domains relate to its functional selectivity has not been demonstrated experimentally. We performed 2-photon dendritic micro-dissection on layer-2/3 pyramidal neurons in mouse primary visual cortex. We found that removing the apical dendritic tuft did not alter orientation-tuning. Furthermore, orientation-tuning curves were remarkably robust to the removal of basal dendrites: ablation of 2-3 basal dendrites was needed to cause a small shift in orientation preference, without significantly altering tuning width. Computational modeling corroborated our results and put limits on how orientation preferences among basal dendrites differ in order to reproduce the post-ablation data. In conclusion, neuronal orientation-tuning appears remarkably robust to loss of dendritic input.
TmDOTP : An NMR- based Thermometer for Magic Angle Spinning NMR Experiments
Authors: Zhang Dongyu , Itin Boris , McDermott Ann E.
Published: March 2019

Solid state NMR is a powerful tool to probe membrane protein structure and motions in native lipid structures. Sample heating, caused by magic angle spinning and radio frequency irradiation in solid state NMR, produces uncertainties in sample temperature and thermal broadening caused by temperature distributions, which can also lead to sample deterioration. To measure the sample temperature in real time, and to quantify thermal gradients and their dependence on radio frequency irradiation or spinning frequency, we use the chemical shift thermometer TmDOTP, a lanthanide complex. Compared to other NMR thermometers (e.g., the proton NMR signal of water), the proton spectrum of TmDOTP exhibits higher thermal sensitivity and resolution. In addition, the H6 proton in TmDOTP has a large chemical shift (−175 ppm at 275 K) and is well resolved from the rest of the proton spectrum. We identified two populations of TmDOTP, with differing temperatures and dependency on the radio frequency irradiation power, within proteoliposome samples. We interpret these populations as arising from the supernatant and the pellet, which is sedimented from the sample spinning. Our results indicate that TmDOTP is an excellent internal standard for monitoring temperatures of biophysically relevant samples without distorting their properties.
B-1 cell-mediated modulation of m1-macrophage profile can ameliorate microbicidal functions and disrupt the evasion mechanisms ofEncephalitozoon cuniculi
Authors: Pereira Adriano , Alvares-Saraiva Anuska Marcelino , de Camargo Konno Fabiana Toshie , Spadacci-Morena Diva Denelle , Perez Elizabeth Cristina , Mariano Mario , Lallo Maria Anete
Published: March 2019

Here, we have investigated the possible effect of B-1 cells on the activity of peritoneal macrophages inE. cuniculiinfection. In the presence of B-1 cells, peritoneal macrophages had an M1 profile with showed increased phagocytic capacity and index, associated with the intense microbicidal activity, increased proinflammatory cytokines production and a higher percentage of apoptotic death. The absence of B-1 cells was associated with a predominance of the M2 macrophages, indicating reduced phagocytic capacity and index, microbicidal activity, proinflammatory cytokine production, and apoptotic death, but equal death rate. In addition, in the M2 macrophages, spores of phagocyticE. cuniculiwith polar tubular extrusion were observed, which is an important mechanism of evasion of the immune response. The results showed the importance of B-1 cells in the modulation of macrophage function againstE. cuniculiinfection, increasing microbicidal activity, and reducing the fungal mechanisms involved in the evasion of the immune response.

Highlights

E. cuniculiphagocytosis and microbicidal activity by macrophages increases in the presence of B-1 cells

M1 macrophage profiles were predominant in the presence of B-1 cells

Extrusion of the polar tubule ofE. cuniculioccur inside M2 macrophages in cultures without B-1 cells

B-1 cells derived phagocytes (B-1CDP) identified with microbicidal activity against spores ofE. cuniculi

Author Summary

The adaptive immune response plays a key role againstEncephalitozoon cuniculi, an opportunistic fungus for T cells immunodeficient patients. The role of B cells and antibody play in natural resistance toEncephalitozoon cuniculiremains unresolved. Previously, we demonstrated that B-1 deficient mice (XID), an important component of innate immunity, were more susceptible to encephalitozoonosis, despite the increase in the number of CD4+and CD8+T lymphocytes. Here we observed that the absence of B-1 cells was associated with a larger population of M2 macrophages, an anti-inflammatory profile, which had lower microbicidal activity and phagocyticE. cuniculispores were seen with the extrusion of the polar tubule, which is an important mechanism of evasion of the immune response. The results showed the importance of B-1 cells in the modulation of macrophage function againstE. cuniculiinfection, increasing microbicidal activity, and reducing the fungal mechanisms involved in the evasion of the immune response.