bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-reciprocal light-harvesting nanoantennae made by nature
Authors: Ting Julian Juhi-Lian
Published: April 2019

Most of our current understanding of mechanisms of photosynthesis comes from spectroscopy. However, the classical definition of a radio antenna can be extended to the optical regime to discuss the function of light-harvesting antennae. Further to our previously proposed model of a loop antenna, we provide several more physical explanations in considering the nonreciprocal properties of light harvesters of bacteria. We explain the function of the nonheme iron at the reaction center and present reasons for each module of the light harvester being composed of one carotenoid, two short α-helical polypeptides, and three bacteriochlorophylls; we also explained the toroidal shape of the light harvester, the upper bound of the characteristic length of the light harvester, the functional role played by the observed long-lasting spectrometric signal, and the observed photon antibunching. Based on these analyses, two mechanisms that might be used by radiation-durable bacteria, Deinococcus radiodurans; and the nonreciprocity of an archaeon, Haloquadratum walsbyi, are analyzed. The physical lessons involved are useful for designing artificial light harvesters, optical sensors, wireless power chargers, passive superPlanckian heat radiators, photocatalytic hydrogen generators, and radiation protective cloaks. In particular, it can predict what kind of particles should be used to separate sunlight into a photovoltaically and thermally useful range to enhance the efficiency of solar cells.
Microstructure-based model of nonlinear ultrasonic response in materials with distributed defects
Authors: Li Yulan , Hu Shenyang , Henager Charles H.
Published: April 2019

Nonlinear ultrasonic technique is one of several promising nondestructive evaluation methods for monitoring the evolution of nanosized defects such as radiation-induced defects in nuclear materials. In this work, a microstructure-based phase-field model of dynamic deformation in elastically nonlinear materials has been developed for investigating the dynamic interaction between distributed defects and a propagating longitudinal sound wave. With the model, the effect of second phase precipitates’ size and properties on the nonlinearity parameter β that describes the magnitude of the 2nd harmonic wave was simulated. The results showed that (1) the nonlinearity parameter β increases as the elastic inhomogeneity increases regardless of whether the precipitates are softer or harder than the matrix; (2) β linearly increases with the increase of lattice mismatch strain; and (3) for a given volume fraction of second phase precipitates, β strongly depends on the precipitate size. The predicted precipitate size dependence of β agrees with the experimental data. These results demonstrate that the developed model enables one to predict the contributions of different nonlinear sources to β, to explain the signal physics behind the measured nonlinear ultrasonic response, and to guide the development of nonlinear ultrasound nondestructive detection of material defects in nuclear reactor materials.
Ordinal partition transition network based complexity measures for inferring coupling direction and delay from time series
Authors: Ruan Yijing , Donner Reik V. , Guan Shuguang , Zou Yong
Published: April 2019

It has been demonstrated that the construction of ordinal partition transition networks (OPTNs) from time series provides a prospective approach to improve our understanding of the underlying dynamical system. In this work, we introduce a suite of OPTN based complexity measures to infer the coupling direction between two dynamical systems from pairs of time series. For several examples of coupled stochastic processes, we demonstrate that our approach is able to successfully identify interaction delays of both unidirectional and bidirectional coupling configurations. Moreover, we show that the causal interaction between two coupled chaotic Hénon maps can be captured by the OPTN based complexity measures for a broad range of coupling strengths before the onset of synchronization. Finally, we apply our method to two real-world observational climate time series, disclosing the interaction delays underlying the temperature records from two distinct stations in Oxford and Vienna. Our results suggest that ordinal partition transition networks can be used as complementary tools for causal inference tasks and provide insights into the potentials and theoretical foundations of time series networks.
Bubble interactions and bursting behaviors near a free surface
Authors: Li Tong , Zhang A-Man , Wang Shi-Ping , Li Shuai , Liu Wen-Tao
Published: April 2019

The strong bubble interactions and bursting behaviors near a free surface are studied numerically with a compressible two-phase flow solver. The interface is captured by the volume of fluid method. We investigate the effects of the dimensionless distance between the bubble and the free surface γf (scaled by the maximum bubble radius) ranging from 0.25 to 1.5. For the nonbursting cases, the essential evolution of the toroidal bubble is well captured, including the splitting, coalescence, and recollapse. Generally, a relatively thin spike is generated at the free surface during the first cycle of the bubble. Subsequently, a wider secondary spike at the base of the first spike is formed during the second bubble cycle, which leads to the formation of the crown-shaped spike. When γf is sufficiently small, the bubble bursts at the free surface and an opening cavity is generated. The pressure inside the cavity and the atmospheric pressure are not balanced immediately, and the pressure difference lasts for a while, causing the inward gas flow and the final closure of the cavity. The gas flow is found to play a vital role in the bubble bursting behaviors, which has not been well understood. By comparing with previous studies, three distinct bursting patterns are identified and discussed.
A three-dimensional smoothed particle hydrodynamics dispersion simulation of polydispersed sediment on the seafloor using a message passing interface algorithm
Authors: Tran-Duc Thien , Phan-Thien Nhan , Khoo Boo Cheong
Published: April 2019

Technical activities on seafloor for harvesting polymetallic nodules result in a displacement of a large amount of sediment, which is convected away from the site by the underlying currents and turbulent diffusion, with a possible impact on the benthic communities living in the neighborhood. To better understand the dispersion mechanism of the resuspended sediment, a smoothed particle hydrodynamics technique augmented by a message passing interface parallel algorithm to address the intensive demand on the three-dimensional simulations is developed. Our numerical results show that the resuspended sediment would occupy a downstream area extending to about 5 km, for a nominal current speed of 5 cm/s. The evolution of the sediment plume occurs mainly along the current direction, while the turbulent diffusion disperses the sediment laterally. Coarse sediment particles are found to return to the seafloor fairly quickly after being resuspended, while fine particles are more persistent in the suspended state and travel much further downstream. In 900 tons of sediment resuspended for 18 h, 318 tons have returned to the bottom at the end of the simulation period. The majority of the deposited sediment is composed of coarse sediment particles (d > 60 μm), and almost half of the deposited sediment is distributed within the harvesting region. The sediment deposition rate reaches up to 48% of the resuspension rate and is still rising after 18 h. The horizontal turbulent diffusivity, which is supposed to be weak at the ocean bottom, does not have any obvious influence on the dispersion of the resuspended sediment; it only slightly reduces the deposition rate.
Theoretical investigation of size, shape, and aspect ratio effect on the LSPR sensitivity of hollow-gold nanoshells
Authors: Shabaninezhad Masoud , Ramakrishna Guda
Published: April 2019

The change in refractive index around plasmonic nanoparticles upon binding to biomolecules is routinely used in localized surface plasmon resonance (LSPR)-based biosensors and in biosensing platforms. In this study, the plasmon sensitivity of hollow gold (Au) nanoshells is studied using theoretical modeling where the influence of shape, size, shell thickness, and aspect ratio is addressed. Different shapes of hollow Au nanoshells are studied that include sphere, disk, triangular prism, rod, ellipsoid, and rectangular block. Multilayered Mie theory and discrete dipole approximation were used to determine the LSPR peak position and LSPR sensitivity as a function of size, shell thickness, shape, and aspect ratio. The change in LSPR peak wavelength per unit refractive index is defined as the sensitivity, and interesting results were obtained from the analysis. The rectangular block and rod-shaped Au nanoshells have shown maximum LSPR sensitivity when compared to other shaped Au nanoshells. In addition, increased sensitivity was observed for higher aspect ratio as well as for smaller shell thicknesses. The results are rationalized based on the inner and outer surface plasmonic coupling.
Magnetocardiography with a 16-channel fiber-coupled single-cell Rb optically pumped magnetometer
Authors: Kim Young Jin , Savukov Igor , Newman Shaun
Published: April 2019

We have constructed a low-cost, portable, high-sensitivity 16-channel optically pumped magnetometer (OPM), operating in the spin-exchange relaxation-free regime, and demonstrated its applications in magnetocardiography (MCG). The decrease in the cost of sensors by an order of magnitude is achieved by the 16-channel operation realized in a single module using a single large flat pancake rubidium vapor cell, broad pump and probe laser beams, and a 16-channel photodiode array. The OPM is also based on a fiber-coupled nearly parallel-beam configuration to facilitate multichannel design and make the system portable. For human MCG experiments, the 16-channel OPM which includes optical components is placed inside a wooden enclosure for laser safety. The enclosure is set on a nonmagnetic table inside a magnetically shielded room, while the lasers and electronics are placed outside the shielding room, to avoid magnetic noise. We show that the 16-channel OPM enables simultaneous imaging of human cardiac activity on a large area of the chest in a single scan. The multichannel capability will accelerate clinical MCG imaging to reduce the procedure time and patient fatigue.
Prawn parade: notes on Macrobrachium australiense Holthius, 1950 climbing vertical concrete overflow steps at Gold Creek Reservoir, Queensland
Authors: Torkkola Janne J. , Hemsley Donna W.
Published: April 2019

The freshwater palaemonid shrimp, Macrobrachium australiense, is widespread throughout eastern Australian freshwater catchments. Population genetic structure suggests limited dispersal ability, despite its broad distribution, with one case of observed springtime climbing migration at Queensland’s Dawson Weir. Here, we describe a second record of observed climbing migration, from Queensland’s Gold Creek Reservoir in August 2018. We discuss the likely causes of these migrations, agreeing with Lee and Fielder’s (1979) assessment of intermittent current stimulus and collective rheotactic response leading to mass climbing towards current source.
The meaning of Old Englishfolcscaruand the compound’s function inBeowulf
Authors: Bammesberger Alfred
Published: April 2019

Ever sinceKemble (1840),buton folcscare(Beowulf, 73a) has been thought to mean ‘with the exception of the common land’. The Old English compoundfolcscaruis reliably attested in poetic texts in the sense ‘tribe, nation’; secondarily the meaning ‘province, land’ may have arisen, but nowhere does the compound convey the special sense ‘common land, commons’. It can be shown that a meaning in the area of ‘tribe’ makes sense at line 73 ofBeowulfas well, but the genitivegumenarefers to bothfolcscareandfeorum. It is quite conceivable that the line provides a distant echo of ancient Germanic customs concerning limitations of royal authority as adumbrated in Tacitus’Germania.
Challenging the concept of pure objectivity in British and Spanish hard news reports
Authors: McCabe Anne , Alonso Belmonte Isabel
Published: April 2019

This article provides a linguistic analysis of facts and viewpoints in a British-Peninsular Spanish sample of newspaper reports written about the Second Lebanon war (2006). Almeida’s (1992) category system for the analysis of factuality and nonfactuality, and Martin and White’s (2005) Appraisal framework were used to analyze journalistic ideological subjectivities underlying all factual statements in the news reports. Results show differences in how writers align their readers based on the political ideology of the newspaper, confirming Patterson and Donsbach’s (1996, 466) conclusion that “partisanship can and does intrude on news decisions, even among journalists who are conscientiously committed to a code of strict neutrality.” Thus, the results of this study are of interest to discourse analysts and media researchers.
Scifotainment
Authors: Zhang Yiqiong
Published: April 2019

This article adopts a multi-analytical perspective to examine engagement in an evolving science communication website. The website has evolved to engage readers from a “verbal nucleus” inherited from traditional news to a “hypermodal nucleus” that caters to the information consumption style of social media, and further to a “scifopost” that integrates social media post into the design. The evolution is driven by the shift from a “deficit model” to a “democracy model” in science communication and a larger cultural shift in the nature of knowledge creation and transmission. Furthermore, the more malleable multimodal resources as compared with verbal resources spearhead the shift from channels for science information to entertainment and engagement, which in turn triggers a similar shift of functions in verbal resources.
How much do U.S. patents disclose?
Authors: Arinas Pellón Ismael
Published: April 2019

U.S. patents, contrary to what may be expected, are essentially vague documents where engagement with the reader is minimized. In general, patent drafters typically exploit several vagueness strategies with the purpose of concealing information that may enable their competitors to claim alternative inventions. Within a Discourse Analysis and Applied and Corpus Linguistics framework, this chapter describes some likely incongruities between the legal requirements for the disclosure of the invention and the actual language used in U.S. patents, and illustrates them with examples from a corpus of 1,001 samples. Finally, linguistic corpus evidence is linked to justifications for non-disclosure provided by scholars from diverse fields such as Applied Linguistics, Rhetoric, Economics, Philosophy, and Law.
Organizational metadiscourse across lecturing styles
Authors: Bernad-Mechó Edgar , Fortanet-Gómez Inmaculada
Published: April 2019

This chapter investigates the use of organizational metadiscourse across three different lecturing styles: reading, conversational and rhetorical (Dudley-Evans 1994). Despite the fact that organizational metadiscourse has not traditionally been considered as conveying engagement, we claim that all metadiscourse can perform this function. Although metadiscourse in spoken lectures has received increasing interest in the last decades, to our knowledge there is no study comparing the use of metadiscourse throughout lecturing styles from a multimodal perspective and highlighting engagement. Following Ädel’s (2010) taxonomy and conducting multimodal analyses on a dataset extracted from lectures in Social Sciences at Yale University’s OpenCourseWare, we set out to research organizational metadiscourse instances and demonstrate their multimodal use across lecturing styles and the engagement they convey.
“Bieste à chief d’oliphant”
Authors: Buquet Thierry
Published: April 2019

La Chevalerie de Judas Macchabée et de ses nobles frères, roman en vers daté de 1285, utilise à
plusieurs reprises les animaux comme motifs narratifs symboliques. Certains animaux (dont l’anabulla un des noms
de la girafe au XIIIe siècle) sont empruntés au Liber de natura rerum (LDNR) de
Thomas de Cantimpré. L’analyse du texte de la Chevalerie et l’illustration de son unique témoin manuscrit (Paris,
BnF Fr. 15104) montre que l’auteur s’est non pas inspiré du texte de Thomas de Cantimpré, mais de l’illustration du manuscrit 320
de Valenciennes (témoin du LDNR), dont le programme iconographique (dont ont été conservées les instructions pour
l’enlumineur en notes marginales) présente des écarts par rapport au contenu textuel – erreurs qui seront transmises dans des
témoins enluminés postérieurs du LDNR. Ainsi, l’anabulla et l’aloy y sont
représentés comme des éléphants, alors qu’il s’agit respectivement d’une girafe et d’un élan. L’auteur de la
Chevalerie décrit dans son roman ces deux animaux comme des éléphants, montrant par-là que sa source n’est
pas le texte latin du LDNR, mais des illustrations “fautives” d’un témoin manuscrit particulier.
“Vez ci au feu la grasse oie!”
Authors: Cobby Anne
Published: April 2019

Food and drink play many different roles in the art of the fabliaux, ranging from more or less brief depictions of
everyday hospitality to significant contributions to plot and especially to trickery. This article focuses primarily on Le Prestre
et Alison, comparing its techniques with those of some other fabliaux. The language of food functions on several levels in this
fabliau: it is a means of characterisation, a sign of status and power, and a narrative motif whereby power relations are first established
and then subverted. Roast goose in particular, along with fish, capons and spices, provides echoes and associations both within and beyond
the text, and forms a focus for the shifting relations as a powerful man is outwitted by women who trade in foodstuffs. As the analysis
proceeds it becomes evident that this fabliau has been undervalued.
The churchman and the fox
Authors: Johnson Joseph R.
Published: April 2019

Known to Roman de Renart scholars as MS I, the manuscript BnF, f. fr. 12584 has received surprisingly little critical attention. The codex was discounted in early but influential appraisals by philologists like Ernest Martin, who characterised its late Renart text as absurdly abridged and useless in the reconstitution of an archetypal original. More favourable assessments of both the Renart text of MS I and its remarkably copious system of illustration have since appeared, especially thanks to the forensic attention of Ettina Nieboer, who proposed an intriguing solution to the many riddles of the copy: it seems to have been commissioned by Guy de Roye, Archbishop of Tours. Over two decades later, however, Nieboer’s analyses remain the most detailed treatments of the codex.

My aim in this article is to call for renewed attention to MS I by exploring the neglected obverse of the abridging and suppressing patterns that Nieboer discovered. I argue that a certain tendency to police the Renart, or render it manageable, can indeed be detected in MS I in the plenitude of its present state: the book opens with a devotional painting of the Virgin Mary and contains extensive maniculae highlighting proverbial material. However, to stop here would be to leave the tale incomplete: the book also stages a pronounced resistance to these systems of control, illustrating across its many folios the sheer impossibility of imposing order upon the Roman de Renart.
Le Physiologus, source d’inspiration pour l’art et la littérature du haut Moyen Âge et du Moyen Âge central
Authors: Leclercq-Marx Jacqueline
Published: April 2019

Que la littérature et l’art du Moyen Âge central contiennent de nombreuses références – directes ou indirectes – au Physiologus est bien connu. Il manque toutefois une vue d’ensemble et synthétique des diverses occurrences qui puisse donner la mesure de leur ampleur, de leur diversité et aussi de certaines de leurs spécificités. En outre, on ignore parfois qu’elles s’insèrent dans une tradition aussi longue que fournie, du moins au niveau textuel. Pour toutes ces raisons, on voudra bien trouver ici une mise en perspective de cette source d’inspiration importante, un certain nombre d’études de cas et d’exemples significatifs de même que quelques réflexions susceptibles de nourrir les études à venir.
Resistance and repression in Zimbabwe: a case study of Zimplats mine workers
Authors: Mutekwe Paddington
Published: April 2019

This article contends that contemporary resistance in the mining sector in Zimbabwe is grounded in everyday acts of resistance and is directed towards power relationships exercised at work. Overt forms of resistance have been waning in Zimbabwe because of various pieces of draconian legislation, and subterranean forms of resistance have been gaining traction and deserve to be studied. Drawing on in-depth interviews and participant observations at Zimplats, the article employs Scott’s concept of the ‘weapons of the weak’, which posits that covert forms of resistance are favourable when open and collective resistance seems dangerous, as a means to understand some of the current dynamics of worker struggles in Zimbabwe.
Adaptive NK cells in people exposed to Plasmodium falciparum correlate with protection from malaria
Authors: Hart Geoffrey T. , Tran Tuan M. , Theorell Jakob , Schlums Heinrich , Arora Gunjan , Rajagopalan Sumati , Sangala A.D. Jules , Welsh Kerry J. , Traore Boubacar , Pierce Susan K. , Crompton Peter D. , Bryceson Yenan T. , Long Eric O.
Published: April 2019

How antibodies naturally acquired during Plasmodium falciparum infection provide clinical immunity to blood-stage malaria is unclear. We studied the function of natural killer (NK) cells in people living in a malaria-endemic region of Mali. Multi-parameter flow cytometry revealed a high proportion of adaptive NK cells, which are defined by the loss of transcription factor PLZF and Fc receptor γ-chain. Adaptive NK cells dominated antibody-dependent cellular cytotoxicity responses, and their frequency within total NK cells correlated with lower parasitemia and resistance to malaria. P. falciparum–infected RBCs induced NK cell degranulation after addition of plasma from malaria-resistant individuals. Malaria-susceptible subjects with the largest increase in PLZF-negative NK cells during the transmission season had improved odds of resistance during the subsequent season. Thus, antibody-dependent lysis of P. falciparum–infected RBCs by NK cells may be a mechanism of acquired immunity to malaria. Consideration of antibody-dependent NK cell responses to P. falciparum antigens is therefore warranted in the design of malaria vaccines.
On Space-Time Quasiconcave Solutions of the Heat Equation
Authors: Chen Chuanqiang , Ma Xinan , Salani Paolo
Published: April 2019

In this paper we first obtain a constant rank theorem for the second fundamental form of the space-time level sets of a space-time quasiconcave solution of the heat equation. Utilizing this constant rank theorem, we can obtain some strictly convexity results of the spatial and space-time level sets of the space-time quasiconcave solution of the heat equation in a convex ring. To explain our ideas and for completeness, we also review the constant rank theorem technique for the space-time Hessian of space-time convex solution of heat equation and for the second fundamental form of the convex level sets for harmonic function.
A tale of four valves: outcome of Brucella endocarditis: a case series
Authors: Kulkarni Suraj Kumar , Bhairappa Shivakumar , Rangan Kapil , P Beeresh
Published: April 2019

Background

Brucellosis is a zoonotic infection. Humans contract brucellosis through inhalation of aerosolized infected particles, or when they come in direct contact with infected animal parts, or on consuming unpasteurised dairy products. It can affect multiple organs and systems. Endocarditis is diagnosed late in the course of the disease with mostly aortic valve involvement with serious morbidity and mortality.

Case summary

We report a case series of four patients with Brucella endocarditis. The first patient presented with fever, malaise, and exertional breathlessness. He underwent aortic valve replacement for refractory heart failure and bulky vegetations after failed medical therapy. The second patient presented with fever, breathlessness New York Heart Association (NYHA) III, with arthralgia, myalgia, anorexia, and weight loss. In view of aortic abscess with impending rupture and compression of left main coronary artery, aortic valve replacement was performed on the 4th day of antibiotic treatment. The third patient presented with fever, fatigue, NYHA II, and developed peripheral embolization but responded to medical treatment alone. The fourth patient presented with intermittent fever for 7 months. During hospitalization, he suffered acute limb ischaemia and stroke with absence of left dorsalis pedis and posterior tibial pulsation. Brucella IgG ELISA was positive. Mitral valve replacement was done subsequently with unremarkable hospital course.

Discussion

Brucellosis is a challenging diagnosis to make. The diagnosis and treatment is often delayed as it presents with non-specific symptoms and signs. Cardiac involvement occurs in only 2% of the cases, but accounts for 80% of the mortality due to brucellosis. Brucella endocarditis should be suspected in cases of endocarditis with negative blood cultures and a risk of exposure. The most accepted treatment for Brucella endocarditis is a combination of antimicrobial therapy with surgery.
Post hatch recovery of a probiotic Enterococcus faecium strain in the yolk sac and intestinal tract of broiler chickens after in ovo injection
Authors: Skjøt-Rasmussen Line , Sandvang Dorthe , Blanch Alfred , Nielsen Jette Mundus , Styrishave Tina , Schnabl Jannie , Brockmann Elke , Beck Chrysta N , Kiess Aaron S
Published: April 2019

Concerns about antibiotic-resistant bacteria and their presence in animal products grow and thus alternatives to use of antibiotics in animal production are being investigated. Probiotics have gained increased focus due to improvements in performance, immune health and pathogen reduction when provided to poultry through feed. These traits may be further improved if probiotics can be provided to the embryo before hatch, before meeting environmental pathogens. The objective was to determine the faith of a probiotic Enterococcus faecium (M74) strain in the yolk sac and intestinal tract of broiler chickens after injection into hatching eggs. E. faecium M74 (1.4 × 107 CFU/egg) was applied in ovo at day 18 of incubation. From 1- and 7-day-old chickens, 20 samples from yolk sac, caecal tonsils and rest of the intestinal tract were subjected to CFU counting. Isolates from a sample subset were typed by pulsed-field gel electrophoresis (PFGE). Enterococci were found in varying numbers: 1.0 × 104–2.2 × 1010 CFU/g. The prevalence of M74 PFGE profiles was high in 1-day-old (88%) and 7-day-old chickens (67%). This demonstrates that the embryos ingested M74 before hatching, that M74 is viable for intestinal colonization through in ovo administration, and that the strain multiplies in the chickens gastrointestinal tract post hatching.
Combinatorial Detection of Conserved Alteration Patterns for Identifying Cancer Subnetworks
Authors: Hodzic Ermin , Shrestha Raunak , Zhu Kaiyuan , Cheng Kuoyuan , Collins Colin C , Cenk Sahinalp S
Published: April 2019

Background

Advances in large-scale tumor sequencing have led to an understanding that there are combinations of genomic and transcriptomic alterations specific to tumor types, shared across many patients. Unfortunately, computational identification of functionally meaningful and recurrent alteration patterns within gene/protein interaction networks has proven to be challenging.

Findings

We introduce a novel combinatorial method, cd-CAP (combinatorial detection of conserved alteration patterns), for simultaneous detection of connected subnetworks of an interaction network where genes exhibit conserved alteration patterns across tumor samples. Our method differentiates distinct alteration types associated with each gene (rather than relying on binary information of a gene being altered or not) and simultaneously detects multiple alteration profile conserved subnetworks.

Conclusions

In a number of The Cancer Genome Atlas datasets, cd-CAP identified large biologically significant subnetworks with conserved alteration patterns, shared across many tumor samples.
Impact of Water Quality, Sanitation, Handwashing, and Nutritional Interventions on Enteric Infections in Rural Zimbabwe: The Sanitation Hygiene Infant Nutrition Efficacy (SHINE) Trial
Authors: Rogawski McQuade Elizabeth T , Platts-Mills James A , Gratz Jean , Zhang Jixian , Moulton Lawrence H , Mutasa Kuda , Majo Florence D , Tavengwa Naume , Ntozini Robert , Prendergast Andrew J , Humphrey Jean H , Liu Jie , Houpt Eric R
Published: April 2019

Background

We assessed the impact of water, sanitation, and hygiene (WASH) and infant and young child feeding (IYCF) interventions on enteric infections in the Sanitation Hygiene Infant Nutrition Efficacy (SHINE) trial in rural Zimbabwe.

Methods

We tested stool samples collected at 1, 3, 6, and 12 months of age and during diarrhea using quantitative molecular diagnostics for 29 pathogens. We estimated the effects of the WASH, IYCF, and combined WASH + IYCF interventions on individual enteropathogen prevalence and quantity, total numbers of pathogens detected, and incidence of pathogen-attributable diarrhea.

Results

WASH interventions decreased the number of parasites detected (difference in number compared to non-WASH arms, –0.07 [95% confidence interval, –.14 to –.02]), but had no statistically significant effects on bacteria, viruses, or the prevalence and quantity of individual enteropathogens after accounting for multiple comparisons. IYCF interventions had no significant effects on individual or total enteropathogens. Neither intervention had significant effects on pathogen-attributable diarrhea.

Conclusions

The WASH interventions implemented in SHINE (improved pit latrine, hand-washing stations, liquid soap, point-of-use water chlorination, and clean play space) did not prevent enteric infections. Transformative WASH interventions are needed that are more efficacious in interrupting fecal–oral microbial transmission in children living in highly contaminated environments.
Characterization of multiresistance gene cfr(C) variants in Campylobacter from China
Authors: Liu Dejun , Li Xing , Liu Weiwen , Yao Hong , Liu Zhihai , Feßler Andrea T , He Junjia , Zhou Yuqing , Shen Zhangqi , Wu Zuowei , Schwarz Stefan , Zhang Qijing , Wang Yang
Published: April 2019

Objectives

To investigate the occurrence, the genetic environment and the functionality of novel variants of the MDR gene cfr(C) in Campylobacter from China.

Methods

A total of 370 Campylobacter isolates of porcine and chicken origin collected from three regions of China in 2015 were screened for cfr(C) by PCR. The phenotypes and genotypes of cfr(C)-positive isolates were investigated by antimicrobial susceptibility testing, PFGE, MLST, S1-PFGE, Southern blotting and WGS. Quantitative RT–PCR was used to compare the expression levels of the cfr(C) variants in their original isolate and clone constructs in Campylobacter jejuni NCTC 11168.

Results

Four (1.1%) porcine Campylobacter coli isolates were positive for cfr(C). They failed to show elevated MICs of phenicols. The deduced Cfr(C) sequences identified exhibited 2–6 amino acid changes compared with the original Cfr(C) reported in the USA. Cloning of the cfr(C) variant genes into C. jejuni NCTC 11168 resulted in ≥32-fold increases in the MICs of phenicols, indicating that the cfr(C) variant genes are functional. The cfr(C)-carrying isolates belonged to three genotypes and WGS analysis revealed the cfr(C) genes were chromosomally located in MDR genomic islands, which contained multiple antibiotic resistance genes of Gram-positive origin.

Conclusions

This study identified chromosomal cfr(C) genes in C. coli isolates from China. They appeared functionally dormant in the original isolates but were fully functional when cloned and expressed in C. jejuni. The cfr(C) genes were co-transferred with other antibiotic resistance genes, possibly from Gram-positive bacteria. These findings reveal new insights into the function and transmission of cfr(C) in Campylobacter.
Optimizing the Patient Experience during Breast Biopsy
Authors: Soo Mary Scott , Shelby Rebecca A , Johnson Karen S
Published: April 2019

For years, breast imaging has been the model in radiology for patient communication, and more recently, it has been a leader in the growing patient- and family-centered approach to care. To maintain high levels of patient satisfaction during image-guided core-needle breast biopsies, the radiologist should understand patient perspectives so that interventions can be developed to manage patient concerns. This article reviews patient perspectives before, during, and after imaging-guided breast biopsies, and it describes strategies to help optimize the experiences of patients as they navigate the process.
Filling an Empty Self: The Impact of Social Exclusion on Consumer Preference for Visual Density
Authors: Su Lei , Wan Echo Wen , Jiang Yuwei
Published: April 2019

This research examines the effect of social exclusion on consumers’ preferences for visual density. Based on seven experimental studies, we reveal that consumers who perceive themselves as socially excluded evaluate products with dense visual patterns more positively than their nonexcluded peers. This effect occurs because social exclusion triggers a feeling of psychological emptiness and dense patterns can provide a sense of being “filled,” which helps to alleviate this feeling of emptiness. This effect is attenuated when consumers physically fill something or experience a feeling of “temporal density” (i.e., imagining a busy schedule with many tasks packed into a short time). These results shed light on consumers’ socially grounded product aesthetic preferences and offer practical implications for marketers, designers, and policy makers.
US Dominance and American Bias in International Relations Scholarship: A View from the Outside
Authors: Goh Evelyn
Published: April 2019

This article responds to the Journal of Global Security Studies special issue on “American Perspectives and Blind Spots on World Politics,” edited by Jeff Colgan. It applauds their significant achievement in offering positivist demonstrations of the bias generated by American assumptions, coding, and preferences, and quantitative demonstration of the systemic and systematic impact of this bias in skewing key assumptions and theories in mainstream US international relations (IR), by selectivizing attention and compromising accuracy. The article pushes the envelope further by arguing that the call to arms is more urgent and more significant than Colgan et al. express. As US hegemony is diluted, the discipline of IR must increasingly account for other parts of the world. Here, cultural bias generates deeper problems with both ontology and epistemology. The article reviews the wider IR field that shows how IR is at once more global and less easily generalizable, driving the imperative to expand the universe of cases for qualitative research. It warns that the problem of US bias and the wider issue of insularity is accentuated by the growing distance between IR scholarship as expressed in top journal publications and “real-world” puzzles and empirical reality—and by ongoing changes in how governments provide state support and funding for IR research and training.
Two classes of EF1-family translational GTPases encoded by giant viruses
Authors: Zinoviev Alexandra , Kuroha Kazushige , Pestova Tatyana V , Hellen Christopher U T
Published: April 2019

Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computational and functional approaches to shed light on their functions. Multiple sequence alignment indicated that these trGTPases clustered into two groups epitomized by members of Mimiviridae and Marseilleviridae, respectively. trGTPases in the first group were more closely related to GTP-binding protein 1 (GTPBP1), whereas trGTPases in the second group were closer to eEF1A, eRF3 and Hbs1. Functional characterization of representative GTPBP1-like trGTPases (encoded by Hirudovirus, Catovirus and Moumouvirus) using in vitro reconstitution revealed that they possess eEF1A-like activity and can deliver cognate aa-tRNAs to the ribosomal A site during translation elongation. By contrast, representative eEF1A/eRF3/Hbs1-like viral trGTPases, encoded by Marseillevirus and Lausannevirus, have eRF3-like termination activity and stimulate peptide release by eRF1. Our analysis identified specific aspects of the functioning of these viral trGTPases with eRF1 of human, amoebal and Marseillevirus origin.
Silicate, Oxide and Sulphide Trends in Neo-Archean Rocks from the Nilgiri Block, Southern India: the Role of Fluids During High-grade Metamorphism
Authors: Samuel Vinod O , Harlov Daniel E , Kwon Sanghoon , Sajeev K
Published: April 2019

The Nilgiri Block, southern India represents an exhumed section of lower, late Archean (2500 Ma) crust. The northern highlands of the Nilgiri Block are characterized by metagabbros with pyroxenite inlayers. A two-pyroxene granulite zone acts as a transition between the metagabbros and charnockites, which are exposed in the central and southern part of the Nilgiri highlands. Thermobarometry results indicate a SW–NE regional trend both in temperature (∼650–800°C) and in pressure (700–1100 MPa) over the Nilgiri highlands. In the charnockites, composite rutile–ilmenite grains are the dominant oxide assemblage. In the two-pyroxene granulites, hemo-ilmenite–magnetite is dominant with coexisting rutile–ilmenite composite grains in a few samples in the vicinity of the boundary with the charnockites. In the metagabbros, hemo-ilmenite–magnetite is the dominant oxide assemblage. The principal sulphide mineral in the charnockite is pyrrhotite with minor pyrite–chalcopyrite exsolution lamellae or blebs. In the two-pyroxene granulites and the metagabbros, the principal sulphide assemblage consists of discrete pyrite grains with magnetite rims and pyrite–pyrrhotite–chalcocopyrite associations. From these observations, a specific oxidation trend is seen. The northern granulite-facies metagabbros and two-pyroxene granulites of the Nilgiri highlands are highly oxidized compared with the charnockites from the central and southern regions. This higher oxidation state is proposed to be the result of highly oxidizing agents (probably as SO3) in low H2O activity grain boundary NaCl saline fluids with a dissolved CaSO4 component present during granulite-facies metamorphism of the metagabbros and two-pyroxene granulites. Eventually these agents became more reducing, owing to the inherent buffering of the original tonalite–granodiorite granitoids at the graphite–CO2 buffer, such that S took the form of H2S during the granulite-facies metamorphism of the charnockites. At the same time, these saline fluids were also responsible the solid-state conversion of biotite and amphibole to orthopyroxene and clinopyroxene in the metagabbro, two-pyroxene granulite, and charnockite.
Using the basic reproduction number to assess the risk of transmission of lumpy skin disease virus by biting insects
Authors: Gubbins Simon
Published: April 2019

In recent years, lumpy skin disease virus (LSDV) has emerged as a major threat to cattle outside Africa, where it is endemic. Although evidence suggests that LSDV is transmitted by the bites of blood sucking arthropods, few studies have assessed the risk of transmission posed by particular vector species. Here this risk is assessed by calculating the basic reproduction number (R0) for transmission of LSDV by five species of biting insect: the stable fly, Stomoxys calcitrans, the biting midge, Culicoides nubeculosus, and three mosquito species, Aedes aegypti, Anopheles stephensi and Culex quinquefasciatus. Parameters relating to mechanical transmission of LSDV were estimated using new analyses of previously-published data from transmission experiments, while vector life history parameters were derived from the published literature. Uncertainty and sensitivity analyses were used to compute R0 for each species and to identify those parameters which influence its magnitude. Results suggest that S. calcitrans is likely to be the most efficient at transmitting LSDV, with Ae. aegypti also an efficient vector. By contrast, C. nubeculosus, An. stephensi, and Cx. quinquefasciatus are likely to be inefficient vectors of LSDV. However, there is considerable uncertainty associated with the estimates of R0, reflecting uncertainty in most of the constituent parameters. Sensitivity analysis suggests that future experimental work should focus on estimating the probability of transmission from insect to bovine and on the virus inactivation rate in insects.
Commercial gene expression tests for prostate cancer prognosis provide paradoxical estimates of race-specific risk
Authors: Creed Jordan H. , Berglund Anders E. , Rounbehler Robert J. , Awasthi Shivanshu , Cleveland John L. , Park Jong Y. , Yamoah Kosj , Gerke Travis A.
Published: April 2019

Background

Commercial gene expression signatures of prostate cancer (PCa) prognosis were developed and validated in cohorts of predominantly European American men (EAM). Limited research exists on the value of such signatures in African American men (AAM), who have poor PCa outcomes. We explored differences in gene expression between EAM and AAM for three commercially available panels recommended by the National Comprehensive Cancer Network for PCa prognosis. Materials and Methods: 232 EAM and 95 AAM patients provided radical prostatectomy specimens. Gene expression was quantified using Nanostring for 60 genes spanning the Oncotype DX Prostate, Prolaris, and Decipher panels. A continuous expression-based risk score was approximated for each. Differential expression, intrapanel co-expression and risk by race were assessed.

Results and limitations

Clinical and pathologic features were similar between AAM and EAM. Differential expression by race was observed for 48% of genes measured, though the magnitudes of expression differences were small. Coexpression patterns were more strongly preserved by race group for Oncotype DX and Decipher versus Prolaris (integrative correlations of 0.87, 0.73, and 0.62, respectively). Poorer prognosis was estimated in EAM versus AAM for Oncotype DX (p < 0.001), whereas no difference in prognosis was predicted between AAM and EAM using Prolaris or Decipher (p > 0.05). Replication of our findings directly on the commercial panels with long-term follow-up is warranted.

Conclusions

Due to observed racial differences across three commercial gene expression panels for PCa prognosis, caution is warranted when applying these panels in clinical decision-making in AAM.
Blue carbon sequestration dynamics within tropical seagrass sediments: Long-term incubations for changes over climatic scales
Authors: Hoe Chuan Chee , Gallagher John Barry , Theng Chew Swee , Zanuri Norlaila Binti Mohd.
Published: April 2019

Determination of blue carbon sequestration in seagrass sediments over climatic time scales relies on several assumptions, such as no loss of particulate organic carbon (POC) after one or two years, tight coupling between POC loss and CO2emissions, no dissolution of carbonates and removal of the stable black carbon (BC) contribution. We tested these assumptions via 500-day anoxic decomposition/mineralisation experiments to capture centennial parameter decay dynamics from two sediment horizons robustly dated as 2 and 18 years old. No loss of BC was detected, and decay of POC was best described for both horizons by near-identical reactivity continuum models. The models predicted average losses of 49% and 51% after 100 years of burial and 20–22 cm horizons, respectively. However, the loss rate of POC was far greater than the release rate of CO2, both before and after accounting for CO2from anoxic particulate inorganic carbon (PIC) production, possibly as siderite. The deficit could not be attributed to dissolved organic carbon or dark CO2fixation. Instead, evidence based on δ13CO2, acidity and lack of sulphate reduction suggested methanogenesis. The results indicate the importance of centennial losses of POC and PIC precipitation and possibly methanogenesis in estimating carbon sequestration rates.
A pipeline to create predictive functional networks: application to the tumor progression of hepatocellular carcinoma
Authors: Folschette Maxime , Legagneux Vincent , Poret Arnaud , Chebouba Lokmane , Guziolowski Carito , Théret Nathalie
Published: April 2019

Background

Integrating genome-wide gene expression patient profiles with regulatory knowledge is a challenging task because of the inherent heterogeneity, noise and incompleteness of biological data. From the computational side, several solvers for logic programs are able to perform extremely well in decision problems for combinatorial search domains. The challenge then is how to process the biological knowledge in order to feed these solvers to gain insights in a biological study. It requires formalizing the biological knowledge to give a precise interpretation of this information; currently, very few pathway databases offer this possibility.

Results

The presented work proposes an automatic pipeline to extract automatically regulatory knowledge from pathway databases and generate novel computational predictions related to the state of expression or activity of biological molecules. We applied it in the context of hepatocellular carcinoma (HCC) progression, and evaluate the precision and the stability of these computational predictions. Our working base is a graph of 3,383 nodes and 13,771 edges extracted from the KEGG database, in which we integrate 209 differentially expressed genes between low and high aggressive HCC across 294 patients. Our computational model predicts the shifts of expression of 146 initially non-observed biological components. Our predictions were validated at 88% using a larger experimental dataset and cross-validation techniques. In particular, we focus on the protein complexes predictions and show for the first time that NFKB1/BCL-3 complexes are activated in aggressive HCC. In spite of the large dimension of the reconstructed models, our analyses over the computational predictions discover a well constrained region where KEGG regulatory knowledge constrains gene expression of several biomolecules. These regions can offer interesting windows to perturb experimentally such complex systems.

Conclusion

This new pipeline allows biologists to develop their own predictive models based on a list of genes. It facilitates the identification of new regulatory biomolecules using knowledge graphs and predictive computational methods. Our workflow is implemented in an automatic python pipeline which is publicly available at https://github.com/LokmaneChebouba/key-pipe and contains as testing data all the data used in this paper.