bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism
Authors: Rambani Aditi , Pantalone Vince , Yang Songnan , Rice J. Hollis , Song Qijian , Mazarei Mitra , Arelli Prakash R. , Meksem Khalid , Stewart C. Neal , Hewezi Tarek
Published: February 2020

DNA methylation is a widespread epigenetic mark that contributes to transcriptome reprogramming during plant–pathogen interactions. However, the distinct role of DNA methylation in establishing resistant and susceptible responses remains largely unexplored.

Here, we developed and used a pair of near‐isogenic lines (NILs) to characterize DNA methylome landscapes of soybean roots during the susceptible and resistant interactions with soybean cyst nematode (SCN; Heterodera glycines). We also compared the methylomes of the NILs and their parents to identify introduced and stably inherited methylation variants.

The genomes of the NILs were substantially differentially methylated under uninfected conditions. This difference was associated with differential gene expression that may prime the NIL responses to SCN infection. In response to SCN infection, the susceptible line exhibited reduced global methylation levels in both protein‐coding genes and transposable elements, whereas the resistant line showed the opposite response, increased global methylation levels. Heritable and novel nonparental differentially methylated regions overlapping with genes associated with soybean response to SCN infection were identified and validated using transgenic hairy root system.

Our analyses indicate that DNA methylation patterns associated with the susceptible and resistant interactions are highly specific and that novel and stably inherited methylation variants are of biological significance.
Potential effects of antibiotic‐induced gut microbiome alteration on blood–brain barrier permeability compromise in rhesus monkeys
Authors: Wu Qiong , Zhang Yingqian , Zhang Yinbing , Xia Chunchao , Lai Qi , Dong Zaiquan , Kuang Weihong , Yang Cheng , Su Dan , Li Hongxia , Zhong Zhihui
Published: February 2020

The blood–brain barrier (BBB) contributes to the maintenance of brain homeostasis. Gut microbiome composition affects BBB development and expression of tight junction proteins in rodents. However, we still do not know if there is any direct effect of gut microbial composition on BBB permeability and function in normal adult animals. In the current study, we determined temporal and spatial changes in BBB permeability of rhesus monkeys receiving amoxicillin‐clavulanic acid (AC) by monitoring the cerebrospinal fluid/serum albumin ratio and the volume transfer constant (Ktrans). We showed that oral, but not intravenous, AC was associated with subsequent significant alteration in gut microbial composition and an increase in BBB permeability in all monkeys, especially in the thalamus area. Acetic and propionic acids might play a pivotal role in this newly found communication between the gut and the central nervous system. Antibiotic‐induced gut microbial composition change, especially the decrease in acetic acid– and propionic acid–producing phyla and genera, might have a potential effect on the increase in BBB permeability, which may contribute to a variety of neurological and psychological diseases.
Transgender pediatric surgical patients—Important perioperative considerations
Authors: Roque Remigio A.
Published: February 2020

Transgender describes a variety of identities in which an individual's gender identity is different from expected based on the sex assigned at birth. In the United States, it is estimated that over 1 million adults and 150 000 youth identify as transgender, with increasing numbers being seen in healthcare and surgical settings. These numbers will continue to rise as visibility and acceptance grow. Current guidelines recommend transition‐related surgeries be reserved for older adolescents and adults. However, this is not the only circumstance in which the pediatric anesthesiologist may find themselves caring for a transgender patient. In order to provide the safest and most affirming care, it is crucial that the pediatric anesthesiologist develop a working knowledge of this unique and vulnerable population, including the potential impacts of gender‐affirming treatment on their perioperative care.
Rice yield formation under high day and night temperatures—A prerequisite to ensure future food security
Authors: Xu Jiemeng , Henry Amelia , Sreenivasulu Nese
Published: February 2020

Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular‐physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.
Non‐structural carbohydrate dynamics associated with antecedent stem water potential and air temperature in a dominant desert shrub
Authors: Guo Jessica S. , Gear Linnea , Hultine Kevin R. , Koch George W. , Ogle Kiona
Published: February 2020

Non‐structural carbohydrates (NSCs) are necessary for plant growth and affected by plant water status, but the temporal dynamics of water stress impacts on NSC are not well understood. We evaluated how seasonal NSC concentrations varied with plant water status (predawn xylem water potential, Ψ) and air temperature (T) in the evergreen desert shrub Larrea tridentata. Aboveground sugar and starch concentrations were measured weekly or monthly for ~1.5 years on 6–12 shrubs simultaneously instrumented with automated stem psychrometers; leaf photosynthesis (Anet) was measured monthly for 1 year. Leaf sugar increased during the dry, premonsoon period, associated with lower Ψ (greater water stress) and high T. Leaf sugar accumulation coincided with declines in leaf starch and stem sugar, suggesting the prioritization of leaf sugar during low photosynthetic uptake. Leaf starch was strongly correlated with Anet and peaked during the spring and monsoon seasons, while stem starch remained relatively constant except for depletion during the monsoon. Recent photosynthate appeared sufficient to support spring growth, while monsoon growth required the remobilization of stem starch reserves. The coordinated responses of different NSC fractions to water status, photosynthesis, and growth demands suggest that NSCs serve multiple functions under extreme environmental conditions, including severe drought.
Early outcomes comparing induction with antithymocyte globulin vs alemtuzumab in two steroid‐avoidance protocols in pediatric renal transplantation
Authors: Puliyanda Dechu P. , Pizzo Helen , Rodig Nancy , Somers Michael J. G.
Published: February 2020

Steroid avoidance in pediatric kidney transplants was found effective with extended daclizumab induction. Upon discontinuation of daclizumab, lymphocyte‐depleting agents became used, with little comparative data. We assessed outcomes in children undergoing low immunologic‐risk deceased donor (DD) kidney transplants using induction with antithymocyte globulin (ATG) compared to alemtuzumab. We reviewed consecutive DD kidney transplants from January 2015 to September 2017 at two pediatric centers that used different lymphocyte‐depleting agents in steroid‐avoidance protocols: ATG (Center A) and alemtuzumab (Center B), with tacrolimus and MMF as maintenance immunosuppression. Anti‐infective prophylaxis was based on center protocol. Over the first year post‐tx, there were similar rates of infections. EBV and BK viremia were comparable though Center A manifested more low‐grade CMV viremia (A 46% vs B 0%; P = .0009) at median onset 1.8 months, followed by early seroconversion. Reduction of immunosuppression did not differ between groups. DSA at 1 year was similar (A 8% vs 13%) with low rates of BPAR. Need for steroid‐based conversion was low. There were no graft losses and no differences in median eGFR at 30, 90, 180, and 365 days. (a) 1‐year graft outcomes are excellent in steroid‐avoidance regimens using ATG or alemtuzumab induction; (b) conversion to steroid‐based therapy is low; (c) alemtuzumab/high‐dose MMF is associated with lower WBC and more GCSF use; (d) alemtuzumab/higher dose MMF results in more diarrhea and azathioprine conversion than ATG/lower dose MMF; (e) CMV viremia is seen more often with ATG use with infection prophylaxis reduction; however, seroconversion occurs promptly.
Heart transplantation in an infant with Williams‐Beuren syndrome and rapidly progressive ischemic cardiomyopathy
Authors: Baez Hernandez Nathanya , Kirk Richard , Davies Ryan , Roumillat Jessica , Sutcliffe David , Bano Maria , Butts Ryan
Published: February 2020

Ischemic cardiomyopathy with resultant refractory HF may occur in patients with WBS, often as the result of coronary involvement with SVAS. The rapid development of arteriopathy at a young age raises concerns regarding transplant candidacy due to progressive stenoses at other arterial sites with potential detrimental impact on long‐term heart graft function. We report a 2‐month‐old male infant diagnosed with mild aortic stenosis during the neonatal period, but subsequently developed rapidly progressive supravalvar and coronary artery stenoses leading to cardiogenic shock due to myocardial ischemia. The presentation led to the diagnosis of WBS. He required prolonged CPR including ECMO therapy. He subsequently underwent LVAD implantation as bridge to transplant and 4 days later heart transplantation. His post‐operative course was complicated by prolonged mechanical ventilation and extended intensive care unit and hospital stays. However, at follow‐up 18 months post‐transplant he continues to have normal graft function with mild, non‐progressive residual coarctation of aorta and non‐progressive moderately hypoplastic pulmonary arteries.
Collective Victimhood and Social Prejudice: A Post‐Holocaust Theory of Anti‐Semitism
Authors: Antoniou Georgios , Dinas Elias , Kosmidis Spyros
Published: February 2020

Anti‐Semitism represents one of the most penetrating forms of prejudice, yet social research has failed to address the causal underpinnings of the phenomenon. To this end, we empirically test the notion that anti‐Semitism builds on the legacy of the Holocaust. Standing as the benchmark for collective suffering, the Holocaust creates competition over recognition of the status of the victim. Upward comparisons between victimized ingroups with other victimized outgroups trigger social prejudice. Victimhood, thus, creates an antagonistic view of the Jews that, in turn, fuels anti‐Semitic prejudice. We test this theory using data from Greece—the European nation with the highest proportion of anti‐Semites—leveraging two survey experiments and a natural experiment. Our results confirm our theoretical expectations, showing that perceived victimhood fuels anti‐Semitism. The findings of our research carry important implications for dealing with anti‐Semitism and for combating various forms of outgroup prejudice.
Racial Residential Segregation, Perceived Neighborhood Conditions, and Self‐Rated Health: The Case of Houston, Texas
Authors: Anderson Kathryn Freeman , Oncken Lindsay
Published: February 2020

Previous research has linked racial residential segregation to a number of poor health outcomes. Yet, the mechanisms that could account for this association remain poorly understood and have seldom been empirically tested in the literature. In an analysis of the Houston area, we test one potential mechanism—perceived neighborhood conditions, as measured by two indices for neighborhood disorder and environmental quality. Using individual‐level health data from a survey of Houston residents and neighborhood‐level sociodemographic data from the U.S. Census, we estimate a series of multilevel models. We find that black and Latino segregation are linked to the perceived neighborhood disorder index, but no such relationship for the environmental quality index. Moreover, we find that both indices are related to poor self‐rated health in that residents who evaluate their neighborhood conditions negatively are more likely to evaluate their health as poor. We also find a direct effect of black and Latino segregation on poor self‐rated health, and that perceived neighborhood disorder partially mediates this relationship. We do not find a mediation effect for environmental quality. The results suggest that in order to improve the health of these communities, both residential segregation and neighborhood conditions need to be addressed.
The Good, the Bad, and the Ugly: Dimensions of Success and Failure in Research Collaboration
Authors: Sacco Timothy
Published: February 2020

Failure is a common experience in society, and analyses of failure have been important for developing social theory. This article analyzes how chemical scientists experience failure in both credited and uncredited research collaborations. Credited work produces the outputs that are evaluated by administrators and analyzed by social scientists. Thus, “credit” is closely tied with visibility in science. But chemical scientists often engage in uncredited collaboration as well. Uncredited collaborations are not opportunities to receive formal credit for one’s work, but chemical scientists still engage in uncredited work in order to meet the metrics by which they are evaluated. Analyzing 106 interviews with chemical scientists, this article builds a framework for understanding success in collaboration. The two dimensions of this framework that shape experience of success and failure are (1) whether a collaboration produced outputs and (2) whether expectations are met. Collaborative expectations often go unmet, but these disappointments rarely undermine collaborations from producing credited outputs. Novice scientists often have positive experiences in uncredited collaboration despite not receiving credit for their work. Success and failure are experienced differently in credited and uncredited collaboration. Institutional pressures often create circumstances for failure in collaborations while also keeping scientists invested in unsuccessful collaborations.
French Yellow Vests (Gilets Jaunes): Similarities and Differences With Occupy Movements
Authors: Shultziner Doron , Kornblit Irit S.
Published: February 2020

The Yellow Vests movement in France was the most widespread and violent protest movement France has seen since 1968. This research highlights the resemblances and dissimilarities between the Yellow Vests and other Occupy movements. We find similarities in movement origins around suddenly revealed economic issues and relative deprivation. We also find that the Yellow Vests resemble other Occupy movements in terms of a combined strategy of a diffused and countrywide occupation of public spaces alongside weekly mass protest, and a lack of central organization and rejection of leadership. The Yellow Vests, however, differ from other Occupy movements in the extreme violence of the weekly demonstrations. Despite its rejection by the media, violence did not affect widespread public approval. In addition, the Yellow Vests achieved most movement objectives in spite of the lack of effective leadership with whom politicians could negotiate.
Can standards save organic farming from conventionalisation? Dynamics of collective projects and rules in a French organic producers’ organisation
Authors: Dufeu Ivan , Le Velly Ronan , Bréchet Jean‐Pierre , Loconto Allison
Published: February 2020

The unintended consequences of standards and certification schemes, particularly their challenges for alternative agri‐food networks, is a core concern of rural sociology. The conventionalisation of organic agriculture is a prime example. In this article, we contribute to this debate by studying standards that organic farmers developed for themselves within a French organic producers’ organisation. We introduce a ‘regulationist theory of collective action’ and show that these farmers crafted specific rules that go beyond the EU regulation, which in turn gave life to their own alternative, collective project. We thus demonstrate that standardisation and certification do not inevitably engender conventionalisation.
Speciation in North American Junonia from a genomic perspective
Authors: Cong Qian , Zhang Jing , Shen Jinhui , Cao Xiaolong , Brévignon Christian , Grishin Nick V.
Published: February 2020

Delineating species boundaries in phylogenetic groups undergoing recent radiation is a daunting challenge akin to discretizing continuity. Here, we propose a general approach exemplified by American butterflies from the genus Junonia Hübner notorious for the variety of similar phenotypes, ease of hybridization, and the lack of consensus about their classification. We obtain whole‐genome shotgun sequences of about 200 specimens. We reason that discreteness emerges from continuity by means of a small number of key players, and search for the proteins that diverged markedly between sympatric populations of different species, while keeping low polymorphism within these species. Being 0.25% of the total number, these three dozen ‘speciation’ proteins indeed partition pairs of Junonia populations into two clusters with a prominent break in between, while all proteins taken together fail to reveal this discontinuity. Populations with larger divergence from each other, comparable to that between two sympatric species, form the first cluster and correspond to different species. The other cluster is characterized by smaller divergence, similar to that between allopatric populations of the same species and comprise conspecific pairs. Using this method, we conclude that J. genoveva (Cramer), J. litoralis Brévignon, J. evarete (Cramer), and J. divaricata C. & R. Felder are restricted to South America. We find that six species of Junonia are present in the United States, one of which is new: Junonia stemosa Grishin, sp.n. (i), found in south Texas and phenotypically closest to J. nigrosuffusa W. Barnes & McDunnough (ii) in its dark appearance. In the pale nudum of the antennal club, these two species resemble J. zonalis C. & R. Felder (iii) from Florida and the Caribbean Islands. The pair of sister species, J. grisea Austin & J. Emmel (iv) and J. coenia Hübner (v), represent the classic west/east U.S.A. split. The mangrove feeder (as caterpillar), dark nudum J. neildi Brévignon (vi) enters south Texas as a new subspecies Junonia neildi varia Grishin ssp.n. characterized by more extensive hybridization with and introgression from J. coenia, and, as a consequence, more variable wing patterns compared with the nominal J. n. neildi in Florida. Furthermore, a new mangrove‐feeding species from the Pacific Coast of Mexico is described as Junonia pacoma Grishin sp.n. Finally, genomic analysis suggests that J. nigrosuffusa may be a hybrid species formed by the ancestors of J. grisea and J. stemosa sp.n.

This published work has been registered on Zoobank, http://zoobank.org/urn:lsid:zoobank.org:act:C6E70C96‐463D‐4E6A‐95CC‐B0384B0EEEBA.
Closure of a hyperextended system in an orogenic lithospheric pop‐up, Western Pyrenees: The role of mantle buttressing and rift structural inheritance
Authors: Saspiturry Nicolas , Allanic Cécile , Razin Philippe , Issautier Benoit , Baudin Thierry , Lasseur Eric , Serrano Olivier , Leleu Sophie
Published: February 2020

The Early Cretaceous hyperextended Mauléon rift is localized in the north‐western Pyrenean orogen. We infer the Tertiary evolution of the Mauléon basin through the restoration of a 153‐km‐long crustal‐scale balanced cross‐section of the Pyrenean belt, which documents at least 67 km (31%) of orogenic shortening in the Western Pyrenees. Initial shortening, accommodated through inversion of inherited crustal structures, led to formation of a pop‐up structure, in which the opposite edges underwent similar shortening with different tectonic reactivation styles, localized versus. distributed. Underthrusting of the Iberian margin accommodated further convergence, forming the Axial Zone antiformal stack of crustal nappes within a lithospheric pop‐up. Thin‐skinned and thick‐skinned structures propagated outward from the heart of this pop‐up, a block of strong mantle acting as a buttress inhibiting complete inversion of the Mauléon rift basin.
Experimental model for removal of snake venom via hemoperfusion in rats
Authors: Oliveira Maximilian Estevan , Campanholi Jéssica , Cavalcante Roberta Lima , Moreno Felipe Silveira , Yoshida Edson Hideaki , Dini Murilo Melo Juste , Aranha Élvio Franco de Camargo , Cogo José Carlos , Dias Lourdes , Hyslop Stephen , Grotto Denise , Hanai‐Yoshida Valquíria Miwa , Oshima‐Franco Yoko
Published: February 2020

Objective

To examine the efficiency of hemoperfusion in removing South American rattlesnake (Crotalus durissus terrificus) venom from rats compared with neutralization by antivenom.

Design

An exploratory experimental investigation in rats involving the injection of snake venom with or without subsequent hemoperfusion or antivenom administration.

Setting

Basic animal research laboratory in a private university.

Animals

Normal, healthy male Wistar rats (0.29‐0.40 kg, 3‐6 months old) from a commercial breeder.

Interventions

Four experimental groups of randomly allocated rats (n = 3/group) were studied: Group 1: rats were injected with a single dose of venom (5 mg/kg, IM, in the right thigh) with no other treatment; blood samples were collected minutes before death to determine leukocyte, platelet, and erythrocyte counts; Group 2 (Control): rats underwent hemoperfusion alone for 60 min using a hemoperfusion cartridge designed for protein adsorption (by granulated charcoal) and protein precipitation (by tannic acid); Group 3 (Venom + antivenom): rats were injected with venom (5 mg/kg, IM) and, 10 min later, were treated with antivenom at the venom:antivenom ratio recommended by the manufacturer; Group 4 (Venom + hemoperfusion): Rats were injected with venom (5 mg/kg, IM) and, 10 min later, were hemoperfused for 60 min. In groups 2‐4, blood samples were collected for leukocyte, platelet, and erythrocyte counts 24 h after venom.

Measurements and Main Results

Rats injected with venom alone (Group 1) developed signs of neurotoxicity and ataxia and died in 9.0 ± 0.43 h but showed no changes in leukocyte or erythrocyte counts. In contrast, there were no deaths in groups 2‐4. The lack of deaths in Groups 3 and 4 indicated that antivenom and hemoperfusion, respectively, protected against the lethal effects of the venom.

Conclusions

Hemoperfusion with a double‐action hemoperfusion cartridge capable of protein adsorption and precipitation protected rats against C. d. terrificus venom.
Geographical distribution and prevalence of tick‐borne encephalitis virus in questing Ixodes ricinus ticks and phylogeographic structure of the Ixodes ricinus vector in Norway
Authors: Vikse Rose , Paulsen Katrine M. , Edgar Kristin Skarsfjord , H.‐O. Pettersson John , Ottesen Preben Skrede , Okbaldet Yohannes Bein , Kiran Nosheen , Lamsal Alaka , Lindstedt Heidi Elisabeth H. , Pedersen Benedikte Nevjen , Soleng Arnulf , Andreassen Åshild K.
Published: February 2020

The tick‐borne encephalitis virus (TBEV), a zoonotic flaviviral infection, is endemic in large parts of Norway and Eurasia. Humans are mainly infected with TBEV via bites from infected ticks. In Norway, the main geographical distribution of ticks is along the Norwegian coastline from southeast (~59°N) and up to the southern parts of Nordland County (~65°N). In this study, we collected ticks by flagging along the coast from Østfold County to Nordland County. By whole‐genome sequencing of the mitochondrial genome of Ixodes ricinus, the phylogenetic tree suggests that there is limited phylogeographic structure both in Norway and in Europe. The overall TBEV prevalence is 0.3% for nymphs and 4.3% for adults. The highest estimated TBEV prevalence in adult ticks was detected in Rogaland and Vestfold County, while for nymphs it is highest in Vestfold, Vest‐Agder and Rogaland. The present work is one of the largest studies on distribution and prevalence of TBEV in ticks in Scandinavia, showing that the virus is wider distributed in Norway than previously anticipated.
Persistent coherence of quantum superpositions in an optimally doped cuprate revealed by 2D spectroscopy
Authors: Novelli Fabio , Tollerud Jonathan O. , Prabhakaran Dharmalingam , Davis Jeffrey A.
Published: February 2020

Measurement of coherent dynamics in quantum materials reveals correlations across different energy scales.
Direct Kerr frequency comb atomic spectroscopy and stabilization
Authors: Stern Liron , Stone Jordan R. , Kang Songbai , Cole Daniel C. , Suh Myoung-Gyun , Fredrick Connor , Newman Zachary , Vahala Kerry , Kitching John , Diddams Scott A. , Papp Scott B.
Published: February 2020

Orthogonal control of both degrees of freedom of a Kerr comb soliton allows high-precision atomic spectroscopy and stabilization.
Superconducting praseodymium superhydrides
Authors: Zhou Di , Semenok Dmitrii V. , Duan Defang , Xie Hui , Chen Wuhao , Huang Xiaoli , Li Xin , Liu Bingbing , Oganov Artem R. , Cui Tian
Published: February 2020

We have successfully realized the synthesis and superconductivity of praseodymium superhydrides above megabar pressures.
Scalable Majorana vortex modes in iron-based superconductors
Authors: Chiu Ching-Kai , Machida T. , Huang Yingyi , Hanaguri T. , Zhang Fu-Chun
Published: February 2020

A simulation study with experimental data analysis shows the presence of multiple Majorana modes in iron-based superconductors.
Local Berry curvature signatures in dichroic angle-resolved photoelectron spectroscopy from two-dimensional materials
Authors: Schüler Michael , De Giovannini Umberto , Hübener Hannes , Rubio Angel , Sentef Michael A. , Werner Philipp
Published: February 2020

Orbital polarization and Berry curvature signatures are mapped out by circular dichroism in angle-resolved photoemission.
Generalized Anderson’s theorem for superconductors derived from topological insulators
Authors: Andersen Lionel , Ramires Aline , Wang Zhiwei , Lorenz Thomas , Ando Yoichi
Published: February 2020

Cooper pairs in unconventional superconductors having extra internal degrees of freedom are protected in an unexpected way.
A new approach to both high safety and high performance of lithium-ion batteries
Authors: Ge Shanhai , Leng Yongjun , Liu Teng , Longchamps Ryan S. , Yang Xiao-Guang , Gao Yue , Wang Daiwei , Wang Donghai , Wang Chao-Yang
Published: February 2020

We present a new battery with high safety and performance, overcoming the materials-based conflict of reactivity versus stability.
An experimental test of the geodesic rule proposition for the noncyclic geometric phase
Authors: Zhou Zhifan , Margalit Yair , Moukouri Samuel , Meir Yigal , Folman Ron
Published: February 2020

This paper describes geometric effects in the evolution of atoms through a double-slit type experiment on an atom chip.
Molecular defect-containing bilayer graphene exhibiting brightened luminescence
Authors: Zhao Xin-Jing , Hou Hao , Ding Peng-Peng , Deng Ze-Ying , Ju Yang-Yang , Liu Shun-He , Liu Yu-Min , Tang Chun , Feng Liu-Bin , Tan Yuan-Zhi
Published: February 2020

Molecular cutout of defect-containing bilayer graphene was achieved by bottom-up synthesis and showed defect-enhanced luminesce.
Seamless multimaterial 3D liquid-crystalline elastomer actuators for next-generation entirely soft robots
Authors: Zhang Yubai , Wang Zhenhua , Yang Yang , Chen Qiaomei , Qian Xiaojie , Wu Yahe , Liang Huan , Xu Yanshuang , Wei Yen , Ji Yan
Published: February 2020

We propose a strategy to make seamless 3D multimaterial entirely soft actuators without the use of tapes or glues.
Three-dimensional graphene nanoribbons as a framework for molecular assembly and local probe chemistry
Authors: Kawai Shigeki , Krejčí Ondřej , Nishiuchi Tomohiko , Sahara Keisuke , Kodama Takuya , Pawlak Rémy , Meyer Ernst , Kubo Takashi , Foster Adam S.
Published: February 2020

3D graphene nanoribbons were synthesized on surfaces for local chemistry conducted with scanning probe microscopy.
Turbulence generation through an iterative cascade of the elliptical instability
Authors: McKeown Ryan , Ostilla-Mónico Rodolfo , Pumir Alain , Brenner Michael P. , Rubinstein Shmuel M.
Published: February 2020

The violent collision of counter-rotating vortices provides new insights on the mechanistic underpinnings of turbulence.
Dose Optimization of Cefpirome Based on Population Pharmacokinetics and Target Attainment during Extracorporeal Membrane Oxygenation
Authors: Kang Soyoung , Jang June Young , Hahn Jongsung , Kim Dasohm , Lee Jun Yeong , Min Kyoung Lok , Yang Seungwon , Wi Jin , Chang Min Jung
Published: February 2020

To obtain the optimal dosage regimen in patients receiving extracorporeal membrane oxygenation (ECMO), we developed a population pharmacokinetics model for cefpirome and performed pharmacodynamic analyses. This prospective study included 15 patients treated with cefpirome during ECMO. Blood samples were collected during ECMO (ECMO-ON) and after ECMO (ECMO-OFF) at predose and 0.5 to 1, 2 to 3, 4 to 6, 8 to 10, and 12 h after cefpirome administration. The population pharmacokinetic model was developed using nonlinear mixed effects modeling and stepwise covariate modeling.
Intravenous and Intraperitoneal Pharmacokinetics of Dalbavancin in Peritoneal Dialysis Patients
Authors: Van Matre E. T. , Teitelbaum I. , Kiser T. H.
Published: February 2020

Dalbavancin offers a possible treatment option for infectious peritonitis associated with peritoneal dialysis (PD) due to its coverage of Gram-positive bacteria and pharmacokinetic properties. We aimed to evaluate the clinical pharmacokinetics (PK) and pharmacodynamics of dalbavancin in a prospective, randomized, open-label, crossover PK study of adult patients with end-stage renal disease ESRD who were receiving PD. Sampling occurred prior to a single 30-min infusion of dalbavancin at 1,500 mg and at 1, 2, 3, 4, and 6 h and 7 and 14 days postadministration.
Importation of Extensively Drug-Resistant Salmonella enterica Serovar Typhi Cases in Ontario, Canada
Authors: Eshaghi Alireza , Zittermann Sandra , Bharat Amrita , Mulvey Michael R. , Allen Vanessa G. , Patel Samir N.
Published: February 2020

A strain of extensively drug-resistant (XDR)
Salmonella enterica
serovar Typhi has caused a large ongoing outbreak in Pakistan since 2016. In Ontario, Canada, 10 cases of mainly bloodstream infections (
n
 = 9) were identified in patients who traveled to Pakistan. Whole-genome sequencing showed that Canadian cases were genetically related to the Pakistan outbreak strain. The appearance of XDR typhoid cases in Ontario prompted a provincial wide alert to physicians to recommend treatment with carbapenems or azithromycin in suspected typhoid cases with travel history to Pakistan.
d
-Methionine and
d
-Phenylalanine Improve Lactococcus lactis F44 Acid Resistance and Nisin Yield by Governing Cell Wall Remodeling
Authors: Wu Hao , Xue Ershu , Zhi Ning , Song Qianqian , Tian Kairen , Caiyin Qinggele , Yuan Lin , Qiao Jianjun
Published: February 2020

As
d
-amino acids play an important role in cell wall synthesis, we analyzed the effects of 19 different
d
-amino acids on
L. lactis
F44, demonstrating that
d
-Met and
d
-Phe can participate in peptidoglycan (PG) synthesis and improve the acid resistance and nisin yield of this strain.
murF
overexpression further increased the levels of
d
-Met and
d
-Phe incorporated into PG and contributed to the acid resistance of the strain. These findings suggest that
d
-Met and
d
-Phe can be incorporated into PG to improve the acid resistance and nisin yield of
L. lactis
, and this study provides new ideas for the enhancement of nisin production.
Differential Response of the Chicken Trachea to Chronic Infection with Virulent Mycoplasma gallisepticum Strain Ap3AS and Vaxsafe MG (Strain ts-304): a Transcriptional Profile
Authors: Kulappu Arachchige Sathya N. , Young Neil D. , Shil Pollob K. , Legione Alistair R. , Kanci Condello Anna , Browning Glenn F. , Wawegama Nadeeka K.
Published: February 2020

Mycoplasma gallisepticum
is the primary etiological agent of chronic respiratory disease in chickens. Live attenuated vaccines are most commonly used in the field to control the disease, but current vaccines have some limitations. Vaxsafe MG (strain ts-304) is a new vaccine candidate that is efficacious at a lower dose than the current commercial vaccine strain ts-11, from which it is derived. In this study, the transcriptional profiles of the trachea of unvaccinated chickens and chickens vaccinated with strain ts-304 were compared 2 weeks after challenge with
M. gallisepticum
strain Ap3AS during the chronic stage of infection.
The Legionella pneumophila Metaeffector Lpg2505 (MesI) Regulates SidI-Mediated Translation Inhibition and Novel Glycosyl Hydrolase Activity
Authors: Joseph Ashley M. , Pohl Adrienne E. , Ball Theodore J. , Abram Troy G. , Johnson David K. , Geisbrecht Brian V. , Shames Stephanie R.
Published: February 2020

Legionella pneumophila
, the etiological agent of Legionnaires’ disease, employs an arsenal of hundreds of Dot/Icm-translocated effector proteins to facilitate replication within eukaryotic phagocytes. Several effectors, called metaeffectors, function to regulate the activity of other Dot/Icm-translocated effectors during infection. The metaeffector Lpg2505 is essential for
L. pneumophila
intracellular replication only when its cognate effector, SidI, is present.
Ribosome Dimerization Protects the Small Subunit
Authors: Feaga Heather A. , Kopylov Mykhailo , Kim Jenny Kim , Jovanovic Marko , Dworkin Jonathan
Published: February 2020

The formation of ribosome dimers during periods of dormancy is widespread among bacteria. Dimerization is typically mediated by a single protein, hibernation-promoting factor (HPF). Bacteria lacking HPF exhibit strong defects in viability and pathogenesis and, in some species, extreme loss of rRNA. The mechanistic basis of these phenotypes has not been determined. Here, we report that HPF from the Gram-positive bacterium
Bacillus subtilis
preserves ribosomes by preventing the loss of essential ribosomal proteins at the dimer interface. This protection may explain phenotypes associated with the loss of HPF, since ribosome protection would aid survival during nutrient limitation and impart a strong selective advantage when the bacterial cell rapidly reinitiates growth in the presence of sufficient nutrients.
Posttranscriptional Regulation of
tnaA
by Protein-RNA Interaction Mediated by Ribosomal Protein L4 in Escherichia coli
Authors: Singh Dharam , Murashko Oleg N. , Lin-Chao Sue
Published: February 2020

Some ribosomal proteins have extraribosomal functions in addition to ribosome translation function. The extraribosomal functions of several r-proteins control operon expression by binding to own-operon transcripts. Previously, we discovered a posttranscriptional, RNase E-dependent regulatory role for r-protein L4 in the stabilization of stress-responsive transcripts. Here, we found an additional extraribosomal function for L4 in regulating the
tna
operon by L4-intergenic spacer mRNA interactions. L4 binds to the transcribed spacer RNA between
tnaC
and
tnaA
and alters the structural conformation of the spacer RNA, thereby reducing the translation of TnaA. Our study establishes a previously unknown L4-mediated mechanism for regulating gene expression, suggesting that bacterial cells have multiple strategies for controlling levels of tryptophanase in response to varied cell growth conditions.
Multicenter Evaluation of the QIAstat-Dx Respiratory Panel for Detection of Viruses and Bacteria in Nasopharyngeal Swab Specimens
Authors: Leber Amy L. , Lisby Jan Gorm , Hansen Glen , Relich Ryan F. , Schneider Uffe Vest , Granato Paul , Young Stephen , Pareja Josep , Hannet Irene
Published: February 2020

The QIAstat-Dx Respiratory Panel (QIAstat-Dx RP) is a multiplex
in vitro
diagnostic test for the qualitative detection of 20 pathogens directly from nasopharyngeal swab (NPS) specimens. The assay is performed using a simple sample-to-answer platform with results available in approximately 69 min. The pathogens identified are adenovirus, coronavirus 229E, coronavirus HKU1, coronavirus NL63, coronavirus OC43, human metapneumovirus A and B, influenza A, influenza A H1, influenza A H3, influenza A H1N1/2009, influenza B, parainfluenza virus 1, parainfluenza virus 2, parainfluenza virus 3, parainfluenza virus 4, rhinovirus/enterovirus, respiratory syncytial virus A and B,
Bordetella pertussis
,
Chlamydophila pneumoniae
, and
Mycoplasma pneumoniae
.
Development of a Sensitive and Rapid Recombinase Polymerase Amplification Assay for Detection of Anaplasma phagocytophilum
Authors: Jiang Le , Ching Philip , Chao Chien-Chung , Dumler J. Stephen , Ching Wei-Mei
Published: February 2020

Human granulocytic anaplasmosis (HGA) is a tick-borne disease caused by the obligate intracellular Gram-negative bacterium
Anaplasma phagocytophilum
. The disease often presents with nonspecific symptoms with negative serology during the acute phase. Direct pathogen detection is the best approach for early confirmatory diagnosis. Over the years, PCR-based molecular detection methods have been developed, but optimal sensitivity is not achieved by conventional PCR while real-time PCR requires expensive and sophisticated instruments.
High-Content Screening, a Reliable System for Coxiella burnetii Isolation from Clinical Samples
Authors: Francis Rania , Mioulane Maxime , Le Bideau Marion , Mati Marie-Charlotte , Fournier Pierre-Edouard , Raoult Didier , Bou Khalil Jacques Yaacoub , La Scola Bernard
Published: February 2020

Q fever, caused by
Coxiella burnetii
, is a worldwide zoonotic disease that may cause severe forms in humans and requires a specific and prolonged antibiotic treatment. Although current serological and molecular detection tools allow a reliable diagnosis of the disease, culture of
C. burnetii
strains is mandatory to assess their susceptibility to antibiotics and sequence their genome in order to optimize patient management and epidemiological studies. However, cultivating this fastidious microorganism is difficult and restricted to reference centers, as it requires biosafety level 3 laboratories and relies on cell culture performed by experienced technicians.
Nanopore Sequencing Reveals Novel Targets for Detection and Surveillance of Human and Avian Influenza A Viruses
Authors: Yip Cyril Chik-Yan , Chan Wan-Mui , Ip Jonathan Daniel , Seng Claudia Win-May , Leung Kit-Hang , Poon Rosana Wing-Shan , Ng Anthony Chin-Ki , Wu Wai-Lan , Zhao Hanjun , Chan Kwok-Hung , Siu Gilman Kit-Hang , Ng Timothy Ting-Leung , Cheng Vincent Chi-Chung , Kok Kin-Hang , Yuen Kwok-Yung , To Kelvin Kai-Wang
Published: February 2020

Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance. The World Health Organization and the Centers for Disease Control and Prevention have recommended using the M gene as the diagnostic gene target for reverse-transcription-PCR (RT-PCR). However, M gene RT-PCR has reduced sensitivity for recent IAV due to novel gene mutations. Here, we sought to identify novel diagnostic targets for the molecular detection of IAV using long-read third-generation sequencing.
Host Mucin Is Exploited by Pseudomonas aeruginosa To Provide Monosaccharides Required for a Successful Infection
Authors: Hoffman Casandra L. , Lalsiamthara Jonathan , Aballay Alejandro
Published: February 2020

One of the first lines of defense present at mucosal epithelial tissues is mucus, which is a highly viscous material formed by mucin glycoproteins. Mucins serve various functions, but importantly they aid in the clearance of pathogens and debris from epithelial barriers and serve as innate immune factors. In this study, we describe a requirement of host monosaccharides, likely derived from host mucins, for the ability of
Pseudomonas aeruginosa
to colonize the intestine and ultimately cause death in
Caenorhabditis elegans
. We also demonstrate that monosaccharides alter the ability of bacteria to bind to both
Caenorhabditis elegans
intestinal cells and human lung alveolar epithelial cells, suggesting that there are conserved mechanisms underlying host-pathogen interactions in a range of organisms. By gaining a better understanding of pathogen-mucin interactions, we can develop better approaches to protect against pathogen infection.
Collaborative Cross Mice Yield Genetic Modifiers for Pseudomonas aeruginosa Infection in Human Lung Disease
Authors: Lorè Nicola Ivan , Sipione Barbara , He Gengming , Strug Lisa J. , Atamni Hanifa J. , Dorman Alexandra , Mott Richard , Iraqi Fuad A. , Bragonzi Alessandra
Published: February 2020

Respiratory infection caused by
P. aeruginosa
is one of the most critical health burdens worldwide. People affected by
P. aeruginosa
infection include patients with a weakened immune system, such as those with cystic fibrosis (CF) genetic disease or non-CF bronchiectasis. Disease outcomes range from fatal pneumonia to chronic life-threatening infection and inflammation leading to the progressive deterioration of pulmonary function. The development of these respiratory infections is mediated by multiple causes. However, the genetic factors underlying infection susceptibility are poorly known and difficult to predict. Our study employed novel approaches and improved mouse disease models to identify genetic modifiers that affect the severity of
P. aeruginosa
lung infection. We identified candidate genes to enhance our understanding of
P. aeruginosa
infection in humans and provide a proof of concept that could be exploited for other human pathologies mediated by bacterial infection.
Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network
Authors: Lima Laís F. O. , Weissman Maya , Reed Micheal , Papudeshi Bhavya , Alker Amanda T. , Morris Megan M. , Edwards Robert A. , de Putron Samantha J. , Vaidya Naveen K. , Dinsdale Elizabeth A.
Published: February 2020

Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral
P. strigosa
. The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.
Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of MultiplePneumocystisSpecies
Authors: Ma Liang , Chen Zehua , Huang Da Wei , Cissé Ousmane H. , Rothenburger Jamie L. , Latinne Alice , Bishop Lisa , Blair Robert , Brenchley Jason M. , Chabé Magali , Deng Xilong , Hirsch Vanessa , Keesler Rebekah , Kutty Geetha , Liu Yueqin , Margolis Daniel , Morand Serge , Pahar Bapi , Peng Li , Van Rompay Koen K. A. , Song Xiaohong , Song Jun , Sukura Antti , Thapar Sabrina , Wang Honghui , Weissenbacher-Lang Christiane , Xu Jie , Lee Chao-Hung , Jardine Claire , Lempicki Richard A. , Cushion Melanie T. , Cuomo Christina A. , Kovacs Joseph A.
Published: February 2020

Pneumocystiscontinues to be a major cause of disease in humans with immunodeficiency, especially those with HIV/AIDS and organ transplants, and is being seen with increasing frequency worldwide in patients treated with immunodepleting monoclonal antibodies. Annual health care associated withPneumocystispneumonia costs ∼$475 million dollars in the United States alone. In addition to causing overt disease in immunodeficient individuals,Pneumocystiscan cause subclinical infection or colonization in healthy individuals, which may play an important role in species preservation and disease transmission. Our work sheds new light on the diversity and complexity of themsgsuperfamily and strongly suggests that the versatility of this superfamily reflects multiple functions, including antigenic variation to allow immune evasion and optimal adaptation to host environmental conditions to promote efficient infection and transmission. These findings are essential to consider in developing new diagnostic and therapeutic strategies.
Emergence of a Plasmid-Encoded Resistance-Nodulation-Division Efflux Pump Conferring Resistance to Multiple Drugs, Including Tigecycline, in Klebsiella pneumoniae
Authors: Lv Luchao , Wan Miao , Wang Chengzhen , Gao Xun , Yang Qiwen , Partridge Sally R. , Wang Yang , Zong Zhiyong , Doi Yohei , Shen Jianzhong , Jia Peiyao , Song Qianhua , Zhang Qianhui , Yang Jun , Huang Xianhui , Wang Minggui , Liu Jian-Hua
Published: February 2020

In an era of increasing concerns about antimicrobial resistance, tigecycline is likely to have a critically important role in the treatment of carbapenem-resistant
Enterobacteriaceae
, the most problematic pathogens in human clinical settings—especially carbapenem-resistant
K.
pneumoniae
. Here, we identified a new plasmid-borne RND-type tigecycline resistance determinant, TMexCD1-TOprJ1, which is widespread among
K. pneumoniae
isolates from food animals.
tmexCD1-toprJ1
appears to have originated from the chromosome of a
Pseudomonas
species and may have been transferred onto plasmids by adjacent site-specific integrases. Although
tmexCD1-toprJ1
still appears to be rare in human clinical isolates, considering the transferability of the
tmexCD1-toprJ1
gene cluster and the broad substrate spectrum of TMexCD1-TOprJ1, further dissemination of this mobile tigecycline resistance determinant is possible. Therefore, from a “One Health” perspective, measures are urgently needed to monitor and control its further spread. The current low prevalence in human clinical isolates provides a precious time window to design and implement measures to tackle this.
A Polar Flagellar Transcriptional Program Mediated by Diverse Two-Component Signal Transduction Systems and Basal Flagellar Proteins Is Broadly Conserved in Polar Flagellates
Authors: Burnham Peter M. , Kolar William P. , Hendrixson David R.
Published: February 2020

Relative to peritrichous bacteria, polar flagellates possess regulatory systems that order flagellar gene transcription differently and produce flagella in specific numbers only at poles. How transcriptional and flagellar biogenesis regulatory systems are interlinked to promote the correct synthesis of polar flagella in diverse species has largely been unexplored. We found evidence for many Gram-negative polar flagellates encoding two-component signal transduction systems with activity linked to the formation of flagellar type III secretion systems to enable production of flagellar rod and hook proteins at a discrete, subsequent stage during flagellar assembly. This polar flagellar transcriptional program assists, in some manner, the FlhF/FlhG flagellar biogenesis regulatory system, which forms specific flagellation patterns in polar flagellates in maintaining flagellation and motility when activity of FlhF or FlhG might be altered. Our work provides insight into the multiple regulatory processes required for polar flagellation.