bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficiency of methionine and cystine utilization by broiler chickens using stable isotopes
Authors: Pacheco Letícia G. , Sakomura Nilva K. , Suzuki Rafael M. , Dorigam Juliano C. P. , Viana Gabriel S. , Leme Bruno B.
Published: November 2019

The aim of this study was to develop a method to determine the efficiency of utilization of Met and Cys using stable isotopes in order to reduce the number of sacrificed animals relative to the comparative slaughter technique. Met and Cys efficiencies were obtained separately and as total SAA values. Twenty‐one 14‐ to 28‐day‐old broiler chickens were fed experimental diets containing different Met:Cys ratios (44:56, 50:50 and 56:44). Birds were given diets with daily supplements of L‐(15N) Met (60 mmol/kg) or L‐(15N2) Cys (35 mmol/kg) throughout the entire experimental period. Excreta were collected daily, and birds were euthanized at the end of the trial to collect feather‐free bodies and feathers. Samples were analysed for 15N and 15N‐Met content. The utilization efficiency for Met, Cys and Met + Cys for feather‐free bodies was 55%, 75%, and 60%, while the efficiencies for feathers were estimated at 96%, 77% and 84% respectively.
Endoscopic retrieval of gastric and oesophageal foreign bodies in 52 cats
Authors: Dollo V. , Chambers G. , Carothers M.
Published: November 2019

Objectives

To assess the outcomes and major complications in cats that require oesophageal and gastric endoscopic foreign body removal.

Materials and Methods

The medical records of 52 cats with oesophageal and gastric foreign bodies that underwent endoscopic foreign body retrieval during a 13‐year period (2006 to 2018) were retrospectively reviewed to characterise the clinical and radiographic signs, endoscopic findings, outcomes and major complications.

Results

Endoscopic foreign body retrieval was successful in 49 of the 52 cats (94.2%). Radiographs confirmed the foreign material in 24 of the 50 cats (48%). Major complications occurred in eight of the 52 cats (15.4%) and included pleural effusion (n=2), aspiration pneumonia (n=2), unsuccessful removal of foreign material with endoscopy (n=3), oesophageal stricture formation (n=3) and cardiopulmonary arrest (n=1). Cats with oesophageal foreign bodies were more likely to experience major complications than those with gastric foreign bodies.

Clinical Significance

Endoscopic foreign body removal in cats was associated with good overall outcomes and a low complication rate in this study sample. These results will help veterinarians better understand the outcomes of endoscopic foreign body removal in cats.
Geographic distribution and environmental risk factors of lymphoma in dogs under primary‐care in the UK
Authors: Schofield I. , Stevens K. B. , Pittaway C. , O'Neill D. G. , Fecht D. , Dobson J. M. , Brodbelt D. C.
Published: November 2019

Objectives

To integrate external data sources with VetCompass postcode data to explore the spatial distribution and examine potential associations with environmental risk factors in dogs diagnosed with lymphoma at primary care veterinary practices.

Materials and Methods

Cases of lymphoma were identified from electronic patient records of 455,553 dogs under primary veterinary care during 2013 in the UK. Cases were defined as either laboratory‐confirmed or non‐laboratory‐confirmed. Disease maps at the postcode‐district level were used to define the geographic distribution of lymphoma incidence and spatial clustering was explored. Environmental risk factors from external data sources were transferred to a compatible format and logistic regression modelling was used to examine associations between environmental herbicide, fungicide and radon concentrations with lymphoma.

Results

From the denominator population of 455,553 dogs, 279 lymphoma cases (187 with laboratory confirmation and 93 without) were identified. Heterogeneous geographic variation was observed with weak evidence of clustering around London and the south‐west of England. Herbicide and fungicide exposures were weakly associated with a diagnosis of lymphoma in the univariable analysis. After accounting for the age at diagnosis and breed in the multivariable analysis, herbicide exposure was associated with a diagnosis of lymphoma.

Clinical Significance

The heterogeneous distribution of lymphoma in UK dogs provides further evidence for geographic variation of lymphoma, perhaps in part associated with underlying environmental risk factors. The results suggest an association between environmental herbicide and canine lymphoma.
Homogeneity effects in natural language semantics
Authors: Križ Manuel
Published: November 2019

Natural language sentences in which a property is ascribed to a plurality of objects have truth conditions that are not complementary with the truth conditions of the negations of such sentences. Starting from this observation, this paper presents an overview of so‐calledhomogeneity effects. Arguably a pervasive feature of natural language, homogeneity has reflexes in various domains and opens up a prospect for a unified analysis of phenomena that were hitherto viewed in quite different terms.
Genome‐wide epigenetic isolation by environment in a widespread Anolis lizard
Authors: Wogan Guinevere O. U. , Yuan Michael L. , Mahler D. Luke , Wang Ian J.
Published: November 2019

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome‐wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population‐level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.
Diving into divergence: Differentiation in swimming performances, physiology and gene expression between locally‐adapted sympatric cichlid fishes
Authors: Raffini Francesca , Schneider Ralf F. , Franchini Paolo , Kautt Andreas F. , Meyer Axel
Published: November 2019

Sympatric speciation occurs without geographical barriers and is thought to often be driven by ecological specialization of individuals that eventually diverge genetically and phenotypically. Distinct morphologies between sympatric populations occupying different niches have been interpreted as such differentiating adaptive phenotypes, yet differences in performance and thus likely adaptiveness between them were rarely tested. Here, we investigated if divergent body shapes of two sympatric crater lake cichlid species from Nicaragua, one being a shore‐associated (benthic) species while the other prefers the open water zones (limnetic), affect cruising (Ucrit) and sprinting (Usprint) swimming abilities – performances particularly relevant to their respective lifestyles. Furthermore, we investigated species differences in oxygen consumption (MO2) across different swimming speeds and compare gene expression in gills and white muscle at rest and during exercise. We found a superior cruising ability in the limnetic Amphilophus zaliosus compared to the benthic Amphilophus astorquii, while sprinting was not different, suggesting that their distinct morphologies affect swimming performance. Increased cruising swimming ability in A. zaliosus was linked to a higher oxygen demand during activity (but not rest), indicating different metabolic rates during exercise ‐ a hypothesis supported by coinciding gene expression patterns of gill transcriptomes. We identified differentially expressed genes linked to swimming physiology, regulation of swimming behaviour and oxygen intake. A combination of physiological and morphological differences may thus underlie adaptations to these species' distinct niches. This complex ecological specialization probably resulted in morphological and physiological trade‐offs that contributed to the rapid establishment and maintenance of divergence with gene flow.
Balancing cost and benefit: How E. coli cleverly averts disulfide stress caused by cystine
Authors: Downs Diana M.
Published: November 2019

Building a robust, stable network must include strategies to minimize perturbations caused by environmental stress, while optimizing cellular fitness. The introduction of oxygen into the Earth's atmosphere brought challenges for the microbes that had evolved enzyme machinery and metabolic network stability in the anoxic world. Unable to generate new enzyme paradigms and metabolic networks de novo, organisms have evolved strategies to neutralize the impact of oxygen that can be added to and integrated into the existing metabolic framework. This issue of Molecular Microbiology includes a paper by Korshunov et al. in which the authors describe an elegant strategy that Escherichia coli has evolved to minimize metabolic stress that results from the acquisition and use of cystine, the oxidized form of cysteine, as a source of cellular sulfur. This study highlights how a strategy involving both cost and benefit can result in a functional, but energy intensive mechanism for this bacterium to thrive in an oxic world.
Nulla Proportio in Concordantia: Catholic Political Theology and the Mystery of Consensus
Authors: van Erp Stephan , Bocken Inigo
Published: November 2019

The main question in this article is whether there is room for a genuine Catholic political theology in a contemporary liberal society. Catholic political theology faces the dilemma that it is either opposed to the autonomy of the political sphere as it has been given shape in liberal society by its totality claim, or that it is not, and thereby loses its plausibility as it does in the case of Catholic Social Teaching. The authors of this article assume that there is a way out of the dilemma, namely by applying the fundamental theological concept of ‘locus theologicus’ to political theology. By viewing the political as a locus theologicus, the question arises: Which political aspects of the theological tradition could qualify as having a critical function in modern liberal society? The proposal in this article is to consider Nicholas of Cusa’s theory of finding consensus. Cusa developed this theory during and in response to the Council of Basel (1431‐1449) in his book De concordantia catholica. The experience of consensus is viewed in this text as an apophatic confirmation of God in the performance of political authority. The way in which Cusa develops the idea of consensus is in sharp contrast with modern liberal thinkers such as John Rawls. Cusa’s theory shares a resemblance with those of modern critics of consensus such as Chantal Mouffe and Jacques Rancière. While these authors do not formulate their criticism theologically, once brought into conversation with Cusa, one can find opportunities of seeing the mystery of consensus as a theological critique.
Chronic isolation stress is associated with increased colonic and motor symptoms in the A53T mouse model of Parkinson’s disease
Authors: Diwakarla Shanti , Finkelstein David I. , Constable Remy , Artaiz Olivia , Di Natale Madeleine , McQuade Rachel M. , Lei Enie , Chai Xin‐yi , Ringuet Mitchell T. , Fothergill Linda J. , Lawson Victoria A. , Ellett Laura J. , Berger Joel P. , Furness John B.
Published: November 2019

Background

Chronic stress exacerbates motor deficits and increases dopaminergic cell loss in several rodent models of Parkinson's disease (PD). However, little is known about effects of stress on gastrointestinal (GI) dysfunction, a common non‐motor symptom of PD. We aimed to determine whether chronic stress exacerbates GI dysfunction in the A53T mouse model of PD and whether this relates to changes in α‐synuclein distribution.

Methods

Chronic isolation stress was induced by single‐housing WT and homozygote A53T mice between 5 and 15 months of age. GI and motor function were compared with mice that had been group‐housed.

Key Results

Chronic isolation stress increased plasma corticosterone and exacerbated deficits in colonic propulsion and whole‐gut transit in A53T mice and also increased motor deficits. However, our results indicated that the novel environment‐induced defecation response, a common method used to evaluate colorectal function, was not a useful test to measure exacerbation of GI dysfunction, most likely because of the reported reduced level of anxiety in A53T mice. A53T mice had lower corticosterone levels than WT mice under both housing conditions, but single‐housing increased levels for both genotypes. Enteric neuropathy was observed in aging A53T mice and A53T mice had a greater accumulation of alpha‐synuclein (αsyn) in myenteric ganglia under both housing conditions.

Conclusions & Inferences

Chronic isolation stress exacerbates PD‐associated GI dysfunction, in addition to increasing motor deficits. However, these changes in GI symptoms are not directly related to corticosterone levels, worsened enteric neuropathy, or enteric αsyn accumulation.
Radiation exposure during cardiac device implantation: Lessons learned from a multicenter registry
Authors: Bru Paul , Dompnier Antoine , Amara Walid , Haddad Georges , Galuscan Gianina , Sagnol Pascal , Steinbach Mathieu , Montagnier Christian , Taieb Jérôme , Beguec Julien , Milhem Antoine ,   on behalf of the CNCH Cardiac Rhythm Group
Published: November 2019

Background

Little data are available about radiation exposure during cardiac electrical device implantation, and no dose reference levels have been published. This multicenter, prospective, observational study assesses patient and staff radiation exposure during cardiac device implantations, and aims at defining dose reference levels.

Methods

Patient demographic, procedural, and radiation data were obtained for 657 procedures from nine institutions. Physician and staff exposure were measured using real‐time dosimeters worn beneath and above lead apron. Statistical analysis included fluoroscopy time (FT), dose‐area product (DAP), and DAP adjusted for FT and body mass index.

Results

Pacemakers and cardioverter defibrillators were implanted in 481 and 176 patients, respectively. Of these, 152 were treated with cardiac resynchronization therapy (CRT). Median FTs were 837s (interquartile range [IQR]: 480‐1323), 117s (IQR: 69‐209), and 101s (IQR: 58‐162), and median DAPs were 1410 (IQR: 807‐2601), 150 (IQR: 72‐338), and 129 (IQR: 72‐332) cGy.cm² for biventricular, dual chamber, and ventricular device implantation, respectively. Dose reference levels correspond to the third quartile values. During CRT, higher exposure was observed with four X‐ray systems than with the two newer and customizable ones (adjusted DAP of 0.90 [IQR: 0.26‐1.01] and 0.29 [IQR: 0.23‐0.39], respectively; P < .001).

Conclusion

Based on real‐life measurements, this multicenter registry provides dose reference levels and may help centers assess radiation exposure. Although biventricular device implantation was responsible for the highest radiation exposure, FT was meaningfully shortened compared to previously reported values. For a same FT, the use of new generators and custom settings has significantly reduced DAP.
Verruciform xanthoma in recessive dystrophic epidermolysis bullosa and keratitis‐ichthyosis‐deafness syndrome: Report of two cases and a review of the literature
Authors: Evan‐Browning Eric , Rork Jillian , O’Donnell Patrick , Elaba Zendee , Deng April , Wiss Karen
Published: November 2019

Verruciform xanthoma is a benign, wart‐like lesion that can clinically mimic squamous cell carcinoma. We describe two teenage patients with severe genodermatoses, recessive dystrophic epidermolysis bullosa (RDEB), and keratitis‐ichthyosis‐deafness (KID) syndrome, respectively, each found to have plaques suspicious for malignancy, later demonstrated on histopathologic examination to be verruciform xanthoma. We discuss the connection between these severe genodermatoses and the suspected pathophysiology of verruciform xanthoma. In addition, we highlight the importance of recognizing verruciform xanthoma as a clinical mimicker of squamous cell carcinoma, for which patients with RDEB and KID syndrome are at increased risk.
Obesity hypoventilation syndrome: Stretching the health dollar
Authors: Singh Bhajan
Published: November 2019

See related Article
Are nontariff measures and tariffs substitutes? Some panel data evidence
Authors: Niu Zhaohui , Milner Chris , Gunessee Saileshsingh , Liu Chang
Published: November 2019

Using new estimates of ad valorem equivalent of nontariff measures (NTMs) over time, this paper examines NTMs and tariffs’ relationship for a sample of 70 economies for 4,949 products at the 6‐digit harmonized system level over the period 2003–2015. A panel data methodology models the lagged adjustment of NTMs to tariffs, consistent with a causal relationship. Trade policy substitution is found when the models are estimated in both levels and changes; with this holding for both OECD and non‐OECD countries, but not for the agriculture sector in OECD countries. Overall, there is a fairly complete substitution between policy instruments in absolute terms.
Productivity Dispersion and Measurement Error
Authors: von Brasch Thomas , Iancu Diana‐Cristina , Skjerpen Terje
Published: November 2019

Several reasons have been put forward to explain the high dispersion of productivity across establishments: quality of management, different input usage and market distortions, to name but a few. Although it is acknowledged that a sizable portion of productivity dispersion may also be due to measurement error, little research has been devoted to identifying how much they contribute. We outline a novel procedure for identifying the role of measurement error in explaining the empirical dispersion of productivity across establishments. The starting point of our framework is the errors‐in‐variable model consisting of a measurement equation and a structural equation for latent productivity. We estimate the variance of the measurement error and subsequently estimate the variance of the latent productivity variable, which is not contaminated by measurement error. Using Norwegian data on the manufacture of food products, we find that about one percent of the measured dispersion stems from measurement error.
Avoiding problems in tunneled dialysis catheter placement
Authors: Agarwal Anil K. , Haddad Nabil , Boubes Khaled
Published: November 2019

Tunneled dialysis catheters (TDCs) remain the predominant vascular access for initiation of hemodialysis (HD) worldwide. TDCs are also utilized in a significant number of prevalent patients for continuation of dialysis and during the periods of complications related to arteriovenous (AV) accesses. TDC placement is a routine procedure, but can be associated with mechanical and infectious complications related to placement. Imaging guidance with ultrasound and fluoroscopy has made the placement of TDC safer and more successful. Adequate operator training, careful technique, utilization of a checklist, and barrier precautions are essential to avoid problems related to TDC placement.
Prevalence and predictors of adolescent linear growth and stunting across the urban–rural gradient in eastern Ethiopia
Authors: Irenso Asnake Ararsa , Dessie Yadeta , Berhane Yemane , Assefa Nega , Canavan Chelsey R. , Fawzi Wafaie W.
Published: November 2019

Objective

To assess the magnitude and factors associated with adolescent linear growth and stunting in two eastern Ethiopian communities.

Methods

This cross‐sectional study was conducted in the urban Harar Health Demographic Surveillance Site (HDSS) and rural Kersa Demographic Surveillance and Health Research Center (KDS‐HRC). Univariate analysis was used to describe the data. Multiple regression models examined predictors of linear growth. Logistic regression was used to examine factors associated with stunting.

Results

The study included 2010 adolescents. The prevalence of stunting was 26.9% (95% CI 24.9, 28.9), with 8.1% among urban adolescents (95% CI 6.5, 9.9) vs. 47.9% among rural ones (95% CI 44.6, 51.1). There was a significant interaction between residence and sex on the risk of stunting [AOR = 4.17 (95% CI 2.66, 9.9), P < 0.001], and height‐for‐age z score (HAZ) (β = −0.51, P < 0.001). For urban adolescents, older age (18 to 19 years) was negatively associated with linear growth (β= −0.29; P < 0.001). In the rural setting, handwashing practice after toileting was positively associated with HAZ (0.62; P < 0.001) and with lower risk of stunting [AOR = 0.51 (95% CI 0.34, 0.76)]. Urban females had significantly higher HAZ than urban males [β = 0.52; P < 0.01)], and a significantly lower risk of stunting [AOR = 0.29 (95% CI 0.18, 0.48)].

Conclusions

There are significant disparities in the magnitude of stunting between urban and rural adolescents. The gender gap in stunting and linear growth, along with a high prevalence of stunting in early adolescence, calls for age‐appropriate and gender‐sensitive interventions. Particular attention and context‐specific interventions are warranted for adolescents in these and similar rural eastern Ethiopian communities.
Screening for iron deficiency in surgical patients based on noninvasive zinc protoporphyrin measurements
Authors: Füllenbach Christoph , Stein Philipp , Glaser Patricia , Triphaus Chris , Lindau Simone , Choorapoikayil Suma , Schmitt Elke , Zacharowski Kai , Hintereder Gudrun , Hennig Georg , Homann Christian , Stepp Herbert , Spahn Gabriela H. , Kaserer Alexander , Schedler Andreas , Meybohm Patrick , Spahn Donat R.
Published: November 2019

BACKGROUND

Approximately every third surgical patient is anemic. The most common form, iron deficiency anemia, results from persisting iron‐deficient erythropoiesis (IDE). Zinc protoporphyrin (ZnPP) is a promising parameter for diagnosing IDE, hitherto requiring blood drawing and laboratory workup.

STUDY DESIGN AND METHODS

Noninvasive ZnPP (ZnPP‐NI) measurements are compared to ZnPP reference determination of the ZnPP/heme ratio by high‐performance liquid chromatography (ZnPP‐HPLC) and the analytical performance in detecting IDE is evaluated against traditional iron status parameters (ferritin, transferrin saturation [TSAT], soluble transferrin receptor–ferritin index [sTfR‐F], soluble transferrin receptor [sTfR]), likewise measured in blood. The study was conducted at the University Hospitals of Frankfurt and Zurich.

RESULTS

Limits of agreement between ZnPP‐NI and ZnPP‐HPLC measurements for 584 cardiac and noncardiac surgical patients equaled 19.7 μmol/mol heme (95% confidence interval, 18.0–21.3; acceptance criteria, 23.2 μmol/mol heme; absolute bias, 0 μmol/mol heme). Analytical performance for detecting IDE (inferred from area under the curve receiver operating characteristics) of parameters measured in blood was: ZnPP‐HPLC (0.95), sTfR (0.92), sTfR‐F (0.89), TSAT (0.87), and ferritin (0.67). Noninvasively measured ZnPP‐NI yielded results of 0.90.

CONCLUSION

ZnPP‐NI appears well suited for an initial IDE screening, informing on the state of erythropoiesis at the point of care without blood drawing and laboratory analysis. Comparison with a multiparameter IDE test revealed that ZnPP‐NI values of 40 μmol/mol heme or less allows exclusion of IDE, whereas for 65 μmol/mol heme or greater, IDE is very likely if other causes of increased values are excluded. In these cases (77% of our patients) ZnPP‐NI may suffice for a diagnosis, while values in between require analyses of additional iron status parameters.
Hepatitis E virus infection in Hong Kong blood donors
Authors: Tsoi Wai‐Chiu , Zhu Xiaomei , To Amanda Pui‐Chi , Holmberg Jerry
Published: November 2019

Background and Objectives

In Hong Kong, the dominant circulating hepatitis E virus (HEV) genotype is type 4, which can cause more severe clinical consequences than type 3. The aim of this study was to determine the HEV prevalence in Hong Kong blood donors.

Materials and Methods

Unlinked donation samples (n = 10 000) collected in March to May 2015 were tested for HEV RNA using the Procleix HEV assay in an individual donation format (IDT). A subset of 2000 samples were tested for IgG and IgM anti‐HEV using the Wantai enzyme‐linked immunosorbent assay (ELISA). Nucleic acid testing (NAT) initial reactive results were retested once, and repeatedly reactive donations were subjected to alternative molecular procedures as confirmation tests.

Results

One in 5000 Hong Kong blood donors was positive for HEV RNA (0·02%). The two RNA positive samples were also IgG and IgM anti‐HEV positive. One of the two RNA positive donors could be sequenced revealing genotype type 4. Anti‐HEV seroprevalence was estimated as 15·5% among all donors. IgG anti‐HEV positive rate for age group 16–20 was 3·1%, and it increased with age to 43·1% for age group 51–60. Sero‐positivity was higher in males (male donors 18·1% vs. female donors 13·2%), but it was mostly due to the difference in a specific age group (41–50).

Conclusion

Hepatitis E virus RNA positive rate of 0·02% was within the reported range of HEV RNA frequency in developed countries. One donor was confirmed to be genotype 4, which is the dominant genotype in circulation in Hong Kong.
Experimental Investigation of Various Regimes of Bubble Formation and Growth—A Theoretical View of Double Coalescence Regime
Authors: Hamidi Amirhossein , Oshaghi Mohammadreza , Afshin Hossein , Firoozabadi Bahar
Published: November 2019

Bubble formation and growth in a liquid is an important process in many industries. Bubble formation regime determines the essential characteristics of the bubble formation process such as bubble volume, shape, and formation time. The formation regime changes from single to double and multiple by increasing the volumetric gas flowrate. In the present research, various regimes of air bubble formation in pure water and glycerin solutions (glycerin 92%, glycerin 96%, and glycerin 100%) were observed by conducting experiments, and they have been defined in terms of the dimensionless Froude (Fr) and Bond (Bo) numbers. The liquids that have been used in the experiments provide a wide range of viscosity from 0.001 to 1.07 Pa·s. However, the surface tension remains approximately constant. In these experiments, relatively small needle sizes (lower than 0.6 mm), Bond numbers smaller than 0.05, and Froude numbers smaller than 70,000 were used, and the boundaries between various regimes were determined. The results indicate that the Froude number associated with the boundaries between various regimes decreases by increasing Bond number. In addition, for a given needle diameter, the air flowrate at which the regime changes from single to double is lower in glycerin solutions than in water. The mentioned flowrate decreases by increasing the liquid viscosity. Finally, based on the governing equations and experimental results of this study, a new correlation has been obtained to estimate the volume of the first bubble at the moment of the detachment in the double coalescence regime.
Investigation Into the Phenomenon of Flow Deviation in the S-Shaped Discharge Passage of a Slanted Axial-Flow Pumping System
Authors: Wang Chaoyue , Wang Fujun , Tang Yuan , Zi Dan , Xie Lihua , He Chenglian , Zhu Quanrong , Huang Congbing
Published: November 2019

A remarkable flow deviation phenomenon exists in the S-shaped discharge passage of a slanted axial-flow pumping system. In order to reveal the characteristics and development process of the deviating flow, numerical simulation was performed for a 15 deg slanted axial-flow pumping system, and the deviating flow was measured on an experimental rig. The details of the deviating flow in the S-shaped discharge passage were obtained. A kind of “unwinding” flow structure similar to that of DNA in biology is found in the S-shaped passage. The special structure is characterized by a “single strand” in which original helical streamlines are almost straightened. The bulk speed of the fluids on the “single strand” on the left side of the passage significantly increases while the swirling strength and the kinetic pressure ratio decrease. Large-scale Dean vortices at the passage bottom interact with high transverse energy gradient fluids at the passage top as water flows into the convex part of the S-shaped passage, which leads to the emergence of the “unwinding” structure. Reverse secondary flows further enlarge the scale of the Dean vortices as water flows into the concave part of the S-shaped passage, which results in the growth of the “unwinding” structure. With the development of the asymmetrical flow structure, an irreversible severe flow deviation problem naturally comes into being.
Revised wavelength-by-wavelength inversion of ellipsometry data of semiconductor thin films
Authors: Gilliot Mickaël , Hadjadj Aomar , Stchakovsky Michel
Published: November 2019

A method is proposed to extract refractive index, extinction coefficient, and thickness of an unknown layer inside a multilayer sample from spectroscopic ellipsometry measurement. The method is a combination of improved standard and new wavelength-by-wavelength (point-by-point) approaches, treating each point of the spectrum sequentially but considering spectral physical constraints on the extracted optical parameters. The inversion is performed first by extracting thickness in the range of transparency, then by extracting refractive index and extinction coefficient over the whole spectral range, and finally by applying a regularization to enforce Kramers–Kronig consistency between refractive index and extinction coefficient, while optimizing the sample structure parameters (thicknesses). The layer needs to be transparent over one part of the considered spectrum, which is the case of most semiconductors, but no other assumption is necessary about its optical constants. Efficiency of the method is illustrated through the typical example of a zinc oxide (ZnO) layer. This method should be helpful in many practical cases of ellipsometry data interpretation.
Geoacoustic inversion of the acoustic-pressure vertical phase gradient from a single vector sensor
Authors: Shi Junjie , Dosso Stan E. , Sun Dajun , Liu Qingyu
Published: November 2019

A vector sensor can provide measurements of ocean acoustic fields in terms of the acoustic pressure and three-dimensional particle velocity, providing potentially highly-informative data for applications such as geoacoustic inversion. This paper applies nonlinear Bayesian inversion to vector sensor data to estimate seabed geoacoustic properties and uncertainties in South China Sea. Linear-frequency-modulated source transmissions, recorded as acoustic pressure and vertical particle velocity, are processed to estimate the vertical phase gradient of acoustic pressure at multiple frequencies as the inversion data. An advantage of this type of data is that it can be modeled without knowledge of the source spectrum, allowing inversion with an unknown source and a single sensor. Geoacoustic inversion of phase-gradient data is carried out and compared to inversion of the vertical acoustic impedance, another type of vector-sensor data, independent of the source spectrum, which has been considered previously. Model selection for the optimal number of seabed sediment layers is carried out using Bayesian information criterion, and parameter estimates, uncertainties, and correlations are calculated using delayed-rejection adaptive Metropolis-Hastings sampling. Results indicate a three-layer seabed model (including the semi-infinite basement), with properties in agreement with independent measurements including a high-resolution seismic profile and surficial sediment type from a core.
Octave stretching phenomenon with complex tones of orchestral instruments
Authors: Jaatinen Jussi , Pätynen Jukka , Alho Kimmo
Published: November 2019

For decades, the phenomenon of subjectively enlarged octaves has been investigated using sinusoidal and synthesized complex tones. The present study elaborates the topic with samples of real orchestra instruments in successive tone listening experiments. Compared to previous research, this study also included a substantially larger number of subjects (N = 36). Examined instrument tones were categorized into five groups based on their acoustic principles. In addition, each group was assessed at three dynamic levels (pp-mf-ff). Collected data were analyzed with tuning stretch curves by applying generalized additive models in the manner of the Railsback curve used to characterize piano tuning. Although the tuning curve modeled for the orchestra instruments was observed to differ slightly from the Railsback curve and typical Steinway D grand piano tuning (Steinway, New York), the stretching trends were qualitatively similar. Deviation from a mathematical equal-tempered scale was prominent. According to statistical analyses, dynamics or musical background of the participant did not affect results significantly, but some instrument groups exhibited differences in the curve extremities. In conclusion, the stretched scale is natural for a human listener and should be used as a reference scale in tuning machines instead of the mathematical equal-tempered scale.
Is the Profession of Sport Psychology an Illusion?
Authors: Martin Jeffrey
Published: November 2019

The overarching purpose of the current article was to examine the status of sport psychology as a profession in 4 ways. First, the author characterizes the profession of sport psychology as an illusion because there is so little demand for sport psychology services and because there are so few full-time practicing sport psychologists. Second, paradoxically, it appears that many people assume that applied sport psychology is a healthy and viable profession, so the author comments on why this is the case. Sidestepping the lack of jobs does a disservice to graduate students who believe they can easily become practicing sport psychologists. Third, it is clear that few athletes or teams want to pay for sport psychology services, so some reasons why this is the case are presented. Fourth, the author speculates about the future of the sport psychology profession, followed by some recommendations that would rectify his claim that the field’s relative silence on this issue does a disservice to students.
Novel Hepatitis B Virus Capsid Assembly Modulator Induces Potent Antiviral Responses
In Vitro
and in Humanized Mice
Authors: Amblard Franck , Boucle Sebastien , Bassit Leda , Cox Bryan , Sari Ozkan , Tao Sijia , Chen Zhe , Ozturk Tugba , Verma Kiran , Russell Olivia , Rat Virgile , de Rocquigny Hugues , Fiquet Oriane , Boussand Maud , Di Santo James , Strick-Marchand Helene , Schinazi Raymond F.
Published: November 2019

Hepatitis B virus (HBV) affects an estimated 250 million chronic carriers worldwide. Though several vaccines exist, they are ineffective for those already infected. HBV persists due to the formation of covalently closed circular DNA (cccDNA)—the viral minichromosome—in the nucleus of hepatocytes. Current nucleoside analogs and interferon therapies rarely clear cccDNA, requiring lifelong treatment.
Emergence of a Plant Pathogen in Europe Associated with Multiple Intercontinental Introductions
Authors: Landa Blanca B. , Castillo Andreina I. , Giampetruzzi Annalisa , Kahn Alexandra , Román-Écija Miguel , Velasco-Amo María Pilar , Navas-Cortés Juan A. , Marco-Noales Ester , Barbé Silvia , Moralejo Eduardo , Coletta-Filho Helvecio D. , Saldarelli Pasquale , Saponari Maria , Almeida Rodrigo P. P.
Published: November 2019

Xylella fastidiosa
is an economically important plant-pathogenic bacterium that has emerged as a pathogen of global importance associated with a devastating epidemic in olive trees in Italy associated with
X. fastidiosa
subspecies
pauca
and other outbreaks in Europe, such as
X. fastidiosa
subspecies
fastidiosa
and
X. fastidiosa
subspecies
multiplex
in Spain and
X. fastidiosa
subspecies
multiplex
in France. We present evidence of multiple introductions of
X. fastidiosa
subspecies
multiplex
, likely from the United States, into Spain, Italy, and France. These introductions illustrate the risks associated with the commercial trade of plant material at global scales and the need to develop effective policy to limit the likelihood of pathogen pollution into naive regions. Our study demonstrates the need to utilize whole-genome sequence data to study
X. fastidiosa
introductions at outbreak stages, since a limited number of genetic markers does not provide sufficient phylogenetic resolution to determine dispersal paths or relationships among strains that are of biological and quarantine relevance.
Viral Attachment to Biotic and Abiotic Surfaces in Seawater
Authors: Yamada Yosuke , Guillemette Ryan , Baudoux Anne-Claire , Patel Nirav , Azam Farooq
Published: November 2019

Viruses play important roles in altering microbial community structure and biogeochemical cycles in marine environments. Viral attachment to nonhost surfaces can influence host viral infection rates; however, the prevalence of viral attachment to nonhost surfaces and the ratio of attached viruses to total viruses are little known. We used coastal seawater viral assemblages and used marine vibriophage (SIO-2) and enterobacteriophages (T2 and T4) as models to investigate their attachment to abiotic and biotic surfaces in seawater. Viral attachment was observed on several surfaces, such as nonhost bacteria, polymers, filters, cover glasses, and tube surfaces. This study cautions against commonly used protocols that require viral incubation and seawater fractionation. More importantly, these results could influence virus-driven biogeochemical cycles and microbial community structure in the ocean.
Elevated Expression of a Functional Suf Pathway in Escherichia coli BL21(DE3) Enhances Recombinant Production of an Iron-Sulfur Cluster-Containing Protein
Authors: Corless Elliot I. , Mettert Erin L. , Kiley Patricia J. , Antony Edwin
Published: November 2019

Large quantities of recombinantly overproduced [Fe-S] cluster-containing proteins are necessary for their in-depth biochemical characterization. Commercially available
E. coli
strain BL21(DE3) and its derivatives have a mutation that inactivates the function of one of the two native pathways (Suf pathway) responsible for cluster biogenesis. Correction of the mutation, combined with sequence changes that elevate Suf protein levels, can increase yield and cluster occupancy of [Fe-S] cluster-containing enzymes, facilitating the biochemical analysis of this fascinating group of proteins.
FliK-Driven Conformational Rearrangements of FlhA and FlhB Are Required for Export Switching of the Flagellar Protein Export Apparatus
Authors: Minamino Tohru , Inoue Yumi , Kinoshita Miki , Namba Keiichi
Published: November 2019

The flagellar type III protein export apparatus coordinates protein export with assembly, which allows the flagellum to be efficiently built at the cell surface. Hook completion is an important morphological checkpoint for the sequential flagellar assembly process. The protein export apparatus switches its substrate specificity from the hook protein to the filament protein upon hook completion. FliK, FlhB, and FlhA are involved in the export-switching process, but the mechanism remains a mystery. By analyzing a slow-cleaving
flhB
(
P270A
) mutant, we provide evidence that an interaction between FliK and FlhB induces conformational rearrangements in FlhB, followed by a structural remodeling of the FlhA ring structure that terminates hook assembly and initiates filament formation.
Diversity in
lac
Operon Regulation among Diverse Escherichia coli Isolates Depends on the Broader Genetic Background but Is Not Explained by Genetic Relatedness
Authors: Phillips Kelly N. , Widmann Scott , Lai Huei-Yi , Nguyen Jennifer , Ray J. Christian J. , Balázsi Gábor , Cooper Tim F.
Published: November 2019

The
lac
operon of
Escherichia coli
is a classic model for studying gene regulation. This study has uncovered features such as the environmental input logic controlling gene expression, as well as gene expression bistability and hysteresis. Most
lac
operon studies have focused on a few lab strains, and it is not known how generally those findings apply to the diversity of
E. coli
strains. We examined the environmental dependence of
lac
gene regulation in 20 natural isolates of
E. coli
and found a wide range of regulatory responses. By transferring
lac
genes from natural isolate strains into a common reference strain, we found that regulation depends on both the
lac
genes themselves and on the broader genetic background, indicating potential for still-greater regulatory diversity following horizontal gene transfer. Our results reveal that there is substantial natural variation in the regulation of the
lac
operon and indicate that this variation can be ecologically meaningful.
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands
Authors: Farrer Rhys A. , Chang Miwha , Davis Michael J. , van Dorp Lucy , Yang Dong-Hoon , Shea Terrance , Sewell Thomas R. , Meyer Wieland , Balloux Francois , Edwards Hannah M. , Chanda Duncan , Kwenda Geoffrey , Vanhove Mathieu , Chang Yun C. , Cuomo Christina A. , Fisher Matthew C. , Kwon-Chung Kyung J.
Published: November 2019

Cryptococcus gattiiis an environmental pathogen that causes severe systemic infection in immunocompetent individuals more often than in immunocompromised humans. Over the past 2 decades, researchers have shown thatC. gattiifalls within four genetically distinct major lineages. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drug-sensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (varietygattiifive). The discovery of a new lineage from an understudied ecological region has far-reaching implications for the study and understanding of fungal pathogens and diseases they cause.
Candida albicans
rvs161
Δ and
rvs167
Δ Endocytosis Mutants Are Defective in Invasion into the Oral Cavity
Authors: Naseem Shamoon , Douglas Lois M. , Konopka James B.
Published: November 2019

Oropharyngeal candidiasis (OPC) is a common fungal infection that is associated with severe morbidity. Another concern is that patients at risk for developing OPC often take long courses of antifungal drugs, which can lead to the emergence of drug-resistant
C. albicans
strains. We therefore identified nine mutants with defects in undergoing invasive hyphal growth in the oral cavity, increasing the number of genes known to be involved in OPC by more than 30%. The two strongest mutants,
rvs161
Δ and
rvs167
Δ, have defects in endocytosis. The
rvs
Δ mutants appear to have a specific defect in initiating invasive growth, as preinducing the cells to form hyphae prior to infection restored their ability to cause OPC. These results indicate that blocking endocytosis could have therapeutic value in preventing the initiation of OPC without leading to development of resistance against drugs currently used to treat fungal infections.
IRG1 and Inducible Nitric Oxide Synthase Act Redundantly with Other Interferon-Gamma-Induced Factors To Restrict Intracellular Replication of Legionella pneumophila
Authors: Price Jordan V. , Russo Daniel , Ji Daisy X. , Chavez Roberto A. , DiPeso Lucian , Lee Angus Yiu-Fai , Coers Jörn , Vance Russell E.
Published: November 2019

Legionella pneumophila
is one example among many species of pathogenic bacteria that replicate within mammalian macrophages during infection. The immune signaling factor interferon gamma (IFN-γ) blocks
L. pneumophila
replication in macrophages and is an essential component of the immune response to
L. pneumophila
and other intracellular pathogens. However, to date, no study has identified the exact molecular factors induced by IFN-γ that are required for its activity. We generated macrophages lacking different combinations of IFN-γ-induced genes in an attempt to find a genetic background in which there is a complete loss of IFN-γ-mediated restriction of
L. pneumophila
. We identified six genes that comprise the totality of the IFN-γ-dependent restriction of
L. pneumophila
replication in macrophages. Our results clarify the molecular basis underlying the potent effects of IFN-γ and highlight how redundancy downstream of IFN-γ is key to prevent exploitation of macrophages by pathogens.
Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India
Authors: Gupta Ankit , Dhakan Darshan B. , Maji Abhijit , Saxena Rituja , P.K. Vishnu Prasoodanan , Mahajan Shruti , Pulikkan Joby , Kurian Jacob , Gomez Andres M. , Scaria Joy , Amato Katherine R. , Sharma Ashok K. , Sharma Vineet K.
Published: November 2019

This study provides novel insights on the CRC-associated microbiome of a unique cohort in India, reveals the potential role of a new bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive diagnosis of CRC. The study gains additional significance, as India is among the countries with a very low incidence of CRC, and the diet and lifestyle in India have been associated with a distinct gut microbiome in healthy Indians compared to other global populations. Thus, in this study, we hypothesize a unique relationship between CRC and the gut microbiome in an Indian population.
Cerebral arteriovenous malformations during pregnancy: a management dilemma
Authors: Sohail Rubina , Bashir Qasim , Kanwal Shahlla , Ali Maryam Iqbal
Published: November 2019

The rupture of a brain cranial arteriovenous malformation (bAVM) has been associated with pregnancy; however, due to scarcity of data about this rare condition, management still remains a dilemma both for obstetricians and neurophysicians. The management plan is decided after weighing the benefits of bAVM treatment against the risk of bleeding in pregnancy. There is consensus on deciding the treatment of ruptured brain AVM during pregnancy based on neurological and not obstetrical indications. The management is decided using a multidisciplinary approach.

We report the case of a primigravida who presented at 15 weeks of gestation with intracranial haemorrhage secondary to ruptured bAVM, which was managed by glue embolisation. However, she presented again after 9 days in a moribund condition with fever, vomiting and malaise. The family was very concerned about the patient. The multidisciplinary team after evaluation of patient decided for hysterotomy based on the deteriorating maternal condition.