bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial patterns in sub‐Arctic benthos: multiscale analysis reveals structural differences between community components
Authors: Silberberger Marc J. , Renaud Paul E. , Buhl‐Mortensen Lene , Ellingsen Ingrid H. , Reiss Henning
Published: June 2018

An important goal for ecosystem‐based management is to protect marine habitats and their associated fauna. Understanding the spatial structure and interrelationships of benthic communities and their underlying environmental drivers, therefore, is of great importance. The benthic community off the sub‐Arctic Lofoten‐Vesterålen islands was studied on multiple spatial scales, using theMEM(Moran's eigenvector maps) framework to identify spatial structure in broadscale (hundreds of kilometers), mesoscale (20 km), and fine‐scale (1.5 km) epifaunal and infaunal communities. A combination of eigenvector‐based multivariate analyses and variation partitioning on multiple sets of explanatory variables was used to identify characteristic species and environmental drivers that have a high importance in structuring the communities. Community structure of both epifauna and infauna strongly reflected the boundary of warm Atlantic (>0.5°C) and cold Arctic water masses (<0.5°C), which coincides approximately with the 800‐m isobath in this region. Apart from this dominant broadscale determinant, epifauna and infauna displayed different spatial patterns and drivers. Both components differ significantly across local marine landscapes; however, this characterization is not sufficient for infauna, where additional sediment characteristics play an important role in structuring the community across all spatial scales. Within marine landscapes (mesoscale), epifauna displays a spatial structure that, for the most part, could not be attributed to any of the included environmental drivers. The case of the Lofoten‐Vesterålen region demonstrated that the used analysis is a valuable tool in spatial planning, as it allows for comparison of the relative importance of individual environmental drivers for the studied faunal components, without losing the information about spatial patterns associated with individual drivers.
Quantifying fear effects on prey demography in nature
Authors: Peers Michael J. L. , Majchrzak Yasmine N. , Neilson Eric , Lamb Clayton T. , Hämäläinen Anni , Haines Jessica A. , Garland Laura , Doran‐Myers Darcy , Broadley Kate , Boonstra Rudy , Boutin Stan
Published: June 2018

In recent years, it has been argued that the effect of predator fear exacts a greater demographic toll on prey populations than the direct killing of prey. However, efforts to quantify the effects of fear have primarily relied on experiments that replace predators with predator cues. Interpretation of these experiments must consider two important caveats: (1) the magnitude of experimenter‐induced predator cues may not be realistically comparable to those of the prey's natural sensory environment, and (2) given functional predators are removed from the treatments, the fear effect is measured in the absence of any consumptive effects, a situation which never occurs in nature. We contend that demographic consequences of fear in natural populations may have been overestimated because the intensity of predator cues applied by experimenters in the majority of studies has been unnaturally high, in some instances rarely occurring in nature without consumption. Furthermore, the removal of consumption from the treatments creates the potential situation that individual prey in poor condition (those most likely to contribute strongly to the observed fear effects via starvation or reduced reproductive output) may have been consumed by predators in nature prior to the expression of fear effects, thus confounding consumptive and fear effects. Here, we describe an alternative treatment design that does not utilize predator cues, and in so doing, better quantifies the demographic effect of fear on wild populations. This treatment substitutes the traditional cue experiment where consumptive effects are eliminated and fear is simulated with a design where fear is removed and consumptive effects are simulated through the experimental removal of prey. Comparison to a natural population would give a more robust estimate of the effect of fear in the presence of consumption on the demographic variable of interest. This approach represents a critical advance in quantifying the mechanistic pathways through which predation structures ecological communities. Discussing the merits of both treatments will motivate researchers to go beyond simply describing the existence of fear effects and focus on testing their true magnitude in wild populations and natural communities.
BATF regulates the expression of Nfil3, Wnt10a and miR155hg for efficient induction of antibody class switch recombination in mice
Authors: Morman Rosemary E. , Schweickert Patrick G. , Konieczny Stephen F. , Taparowsky Elizabeth J.
Published: June 2018

BATF functions in T cells and B cells to control the host response to antigen and promote the production of class switched immunoglobulins. In this study, we demonstrate that BATF expression increases rapidly, and transiently, following B cell stimulation and use an inducible murine model of BATF deletion to show that this induction is necessary, and sufficient, for immunoglobulin (Ig) class switch recombination (CSR). We examine two genes (Nfil3 and miR155gh) that are positively regulated, and one gene (Wnt10a) that is negatively regulated by BATF during CSR. These genes play essential roles in CSR and each impacts the expression and/or function of the others. Our observations allow these targets of BATF regulation to be positioned in a network upstream of the activation of germline transcripts (GLT) from the IgH locus and of transcriptional activation of Aicda – the gene encoding the enzyme directing Ig gene rearrangements. This work extends the knowledge of the molecular control of CSR and, importantly, positions the induction and function of BATF as an early event in this process.
Monocycle‐like Molecular Rotor Induces a Dielectric Relaxation and Dielectric Phase Transformation in an Organic–Inorganic Hybrid Supermolecule
Authors: Tong Yuan‐Bo , Tian Zheng‐Fang , Duan Hai‐Bao , Zhu Zhong‐Peng , Hong Tian‐Yu , Yang Jing‐Kui
Published: June 2018

A new strategy for the construction of crystalline supermolecular rotors is presented. We obtained the hybrid crystal [(18‐Crown‐6)K]3[NH2(CH3)2]2(Bi2Cl11)·2DMF (1) by introducing the flexible 18‐crown‐6 into the inorganic [Bi2Cl11]5– binuclear anion cluster lattice through the KCl (screw) to connect the organic molecule with inorganic component, in which the coordinated DMF (N,N‐Dimethylformamide) molecule functions as an polar rotator with monocycle shape, revealed by its significant dielectric relaxation above 358 K. The hybrid solid also exhibits dielectric phase transformation and conductivity switch around 413 K, the response mechanism was investigated by variable‐temperature X‐ray single crystal and powder diffraction as well as DSC, TG techniques. The analysis results reveal that the dielectric anomaly and conductivity switch are triggered by the losing of DMF molecules which is fixed with the [(18‐Crown‐6)K]+. And the ionic conductivity reach to 1.10 × 10–3 S cm–1 at 473 K. The interesting molecular structure and molecular thermal motion feature are promising application in the field of artificial molecular machine and dielectric switch.
Continuous‐Flow retro‐Diels–Alder Reaction: A Process Window for Designing Heterocyclic Scaffolds
Authors: Nekkaa Imane , Palkó Márta , Mándity István M. , Miklós Ferenc , Fülöp Ferenc
Published: June 2018

The synthesis of racemic and enantiopure tricyclic and tetracyclic pyrrolopyrimidinones, pyrimidoisoindoles, and spiropyrimidinones, as valuable new chemical entities (NCE), based on a highly controlled continuous‐flow (CF) retro‐Diels–Alder protocol is presented. This approach ensures enhanced safety, and gave the target pyrimidinone derivatives 17–25 in yields higher than those obtained in batch and microwave processes. These results were achieved through careful optimization of the reaction parameters. We also developed an alternative time‐efficient route for the synthesis of intermediate quinazolinones 2–16 involving a three‐step domino ring‐closure reaction followed by spirocyclization under continuous‐flow conditions, starting from β‐aminonorbornene carboxamides 1a–1d and γ‐keto acids or cycloalkanones.
Micro‐Tubular Flow Cell Design Utilizing Commercial Hollow Fiber Dialysis Membranes for Size‐Exclusion Based Flow Batteries
Authors: Stolze C. , Janoschka T. , Winsberg J. , Strumpf M. , Hager M. D. , Schubert U. S.
Published: June 2018

A micro‐tubular flow cell (μTFC) is presented as a novel approach for flow cell design, which differs from previous tubular approaches by its lower cell diameter (3 mm) and half‐cell thicknesses (≤850 μm). Analytical expressions for the ohmic resistances of both micro‐tubular and conventional filter‐press flow cells (cFFC) are derived, which imply that optimized μTFCs can be expected to have an at least two‐fold lower ohmic resistance compared to equally sized cFFCs in the future. The theoretical findings motivate the experimental realization of a first μTFC single‐cell unit to investigate the basic feasibility of this approach. This investigation is enabled by the utilization of a redox‐active polymer in conjunction with a commercially available micro‐tubular dialysis membrane (diameter: 1 mm). Aqueous solutions of poly(2,2,6,6‐tetramethylpiperidin‐4‐yl methacrylate‐co‐poly(ethylene glycol)methyl ether methacrylate) (positive half‐cell) and the Zn/Zn2+ redox couple (negative half‐cell) are utilized as model electrolytes to examine the electrochemical performances of this first μTFC prototype. Furthermore, the common usage of area current densities based on the geometric area of the flow cell is critically discussed. A current density based on the cell volume is suggested as a less ambiguous and, hence, a more reliable parameter for performance evaluation.
Evaluating erosion control practices in an actively gullying watershed in the highlands of Ethiopia
Authors: Ayele Getaneh K. , Addisie Meseret B. , Langendoen Eddy J. , Tegegne Nigus H. , Tilahun Seifu A. , Moges Mamaru A. , Nicholson Charles F. , Steenhuis Tammo S.
Published: June 2018

Soil erosion, with significant contributions from gullies, is a serious problem in the Ethiopian highlands. The objective of this paper is to examine patterns of discharge and sediment transport in the Ethiopian highlands, and to provide an initial assessment of whether soil and water conservation practices (SWCP) can reduce sediment loads in watersheds with actively eroding gullies. The study was conducted in the 414‐ha Ene‐Chilala watershed with a unimodal sub‐humid monsoon climate and actively eroding gullies in the valley bottoms. In 2013 and 2014, the local community was mandated to install upland infiltration furrows and farmers voluntarily rehabilitated six gully heads and protected 16 m of eroding stream banks. Discharge and sediment concentration were measured in two upslope watersheds and at the outlet. Since median infiltration capacity in the uplands was always greater than the rainfall intensity, saturation excess and interflow were main runoff pathways. After 175 mm cumulative rainfall, the groundwater table reached the surface in the valley bottoms, restricting infiltration, and runoff was generated as saturation excess overland flow and flowed through active gullies out of the watershed. Upland rill erosion on ploughed land early in the rain phase, and gully erosion in saturated valley bottoms thereafter, were sources of sediment in the rivers. The mandated infiltration furrows installed on the contour overtopped and damaged cropland. The off‐contour furrows increased streamflow. Gully rehabilitation of an upland gully effectively reduced stream sediment concentration in the upland weir. However, there was little benefit at the watershed outlet since the stream picked up the unconsolidated sediment from the failing banks in the downstream porting of the watershed. Therefore, soil conservation programs that in addition to installing upland practices, rehabilitate the main sediment source (gullies) appear to be the most effective approach to reducing in‐stream suspended sediment concentrations. © 2018 John Wiley & Sons, Ltd.
Joint distributed cell association and interference management in OFDMA‐based heterogeneous networks
Authors: Chinipardaz Maryam , Noorhosseini Majid
Published: June 2018

Considering the ever‐growing demand for network traffic, increasing the capacity of cellular networks has always been a necessity. Heterogeneous cellular networks using small‐scale base stations in addition to macro base stations (BSs) are a low cost and effective solution to this problem. The diversity of the BSs in heterogeneous networks, however, has raised new issues in terms of cell association and interference management compared with the traditional single‐tier networks. Devising novel and effective methods for cell association and resource allocation in these networks is currently an open and developing problem. This paper addresses cell and subband association in the downlink of orthogonal frequency‐division multiple‐access heterogeneous networks. Unlike the existing works in this field, our scheme maximizes network utility while preventing harmful interference for all connections in the network. Using the protocol interference model, necessary and sufficient constraints for preventing interference in cellular networks are presented. By choosing the appropriate interference constraint, the joint problem of cell and subband association is formulated as an integer optimization problem. After simplifying the optimization problem, an equivalent linear problem is obtained. Using one‐level dual decomposition, an iterative algorithm with a near‐optimal solution has been devised. A distributed protocol is then presented, in which each user and each BS requires only its own local data to determine its connection for service. The simulation results demonstrate the algorithm behavior and confirm the efficiency and near‐optimality of the proposed solution.
Correlates of depressive symptoms among older adults living with HIV
Authors: Avila‐Funes José Alberto , Zamudio‐Rodríguez Alfonso , Muñoz‐Nevárez Luis Arnoldo , Belaunzarán‐Zamudio Pablo Francisco , Díaz‐Ramos Julio Alberto , Alcala‐Zermeno Juan Luis , Ouvrard Camille , Sierra‐Madero Juan , Amieva Hélène
Published: June 2018

Objective

To establish the correlates of depressive symptoms among Mexican community‐dwelling older people living with HIV (PLWHIV).

Methods

Cross‐sectional, 2‐center study of 328 participants aged 50 or older being followed in the outpatient HIV clinics of 2 tertiary care hospitals in Mexico. Data were obtained through a comprehensive geriatric assessment. Multivariate logistic regression analyses were performed to identify the correlates of depressive symptoms.

Results

Mean age of participants was 58.4 years (SD = 7.2), and 82.9% were men. Depressive symptoms were present in 15.9% of participants. The multivariate logistic regression models showed that frailty and disability for activities of daily living were both independently associated with depressive symptoms.

Conclusion

Frailty and disability were independent correlates of depressive symptoms in older PLWHIV. Future studies should attempt to explore the role of physical frailty and disability on psychosocial morbidity among older PLWHIV.
Long‐term impacts of early‐life exposure to malaria: Evidence from Taiwan's Eradication Campaign in the 1950s
Authors: Shih Hsiu‐Han , Lin Ming‐Jen
Published: June 2018

This paper utilizes the eradication campaign in Taiwan in the 1950s to estimate the long‐term impacts of early‐life (in utero and postnatal) exposure to malaria. Matching adults in the 1992–2012 Taiwan Social Change Survey to the malaria intensity in their individual place and year of birth, difference‐in‐difference estimation shows strong evidence that the eradication increased men's own educational attainment as well as their family income in adulthood. We also use the 1980 census data to show there was a sharp education increase after the eradication. Furthermore, the eradication increased the educational attainment of married men's spouses. Finally, quantile regressions show that the effect concentrated on the lower percentile of the income distribution. Overall, our results suggest negative effects of early‐life exposure to malaria.
Systematic review of histological remission criteria in eosinophilic esophagitis
Authors: Eke Ransome , Li Tong , White Anna , Tariq Tooba , Markowitz Jonathan , Lenov Andrey
Published: June 2018

Elemental diets, dietary elimination, and steroid therapies are the most common therapies in the clinical trials for eosinophilic esophagitis (EoE). Histological findings (usually reported as eosinophils per microscopic high‐powered field [hpf]) remain the most common end‐point used to define response. Yet, the threshold for defining “response” and “remission” are ill‐defined among consensus guidelines and may vary from study to study. We conducted a systematic literature review of articles on eosinophilic esophagitis, published between January 2007 and November 2017, considering histological remission as the primary outcome. We abstracted treatment information and definitions of histological remission or response. A comparison of definitions of histological remission across and within institutions was performed. A total of 61 articles were included in this review, with approximately 60% of the studies published from centers in the United States. Histological definitions of remission of EoE ranged from 0 to ≤20 eosinophils/hpf. The most stringent criteria, ranging from 0 to ≤5 eosinophils/hpf, were commonly used in interventional trial studies that examined the effects of new treatments. We found remarkable variability in definitions between studies, treatment types, and regions. Age or epidemiological distribution of study subjects did not influence the criteria for histological remission. Clinical and histological improvements are important measures of the effects of treatment. Histological findings, the most objective measure of treatment, should provide an optimal method for comparing the effectiveness of various treatments. Yet, our findings suggest a lack of consistent remission criteria in published studies. Considering these inconsistencies, it is difficult to compare the effectiveness of various treatments.
Bad news for chordal partitions
Authors: Scott Alex , Seymour Paul , Wood David R.
Published: June 2018

Reed and Seymour [1998] asked whether every graph has a partition into induced connected nonempty bipartite subgraphs such that the quotient graph is chordal. If true, this would have significant ramifications for Hadwiger's Conjecture. We prove that the answer is “no.” In fact, we show that the answer is still “no” for several relaxations of the question.
Antimagic orientations of even regular graphs
Authors: Li Tong , Song Zi‐Xia , Wang Guanghui , Yang Donglei , Zhang Cun‐Quan
Published: June 2018

A labeling of a digraph D with m arcs is a bijection from the set of arcs of D to . A labeling of D is antimagic if no two vertices in D have the same vertex‐sum, where the vertex‐sum of a vertex for a labeling is the sum of labels of all arcs entering u minus the sum of labels of all arcs leaving u. Motivated by the conjecture of Hartsfield and Ringel from 1990 on antimagic labelings of graphs, Hefetz, Mütze, and Schwartz [On antimagic directed graphs, J. Graph Theory 64 (2010) 219–232] initiated the study of antimagic labelings of digraphs, and conjectured that every connected graph admits an antimagic orientation, where an orientation D of a graph G is antimagic if D has an antimagic labeling. It remained unknown whether every disjoint union of cycles admits an antimagic orientation. In this article, we first answer this question in the positive by proving that every 2‐regular graph has an antimagic orientation. We then show that for any integer , every connected, 2d‐regular graph has an antimagic orientation. Our technique is new.
Circulating microRNA‐122 levels are important predictor of hepatitis B virus surface antigen seroclearance
Authors: Akuta Norio , Suzuki Fumitaka , Kobayashi Mariko , Hosaka Tetsuya , Fujiyama Shunichiro , Kawamura Yusuke , Sezaki Hitomi , Kobayashi Masahiro , Saitoh Satoshi , Suzuki Yoshiyuki , Arase Yasuji , Ikeda Kenji , Kumada Hiromitsu
Published: June 2018

It is currently unclear what impact serum microRNA‐122 (miR‐122) levels have on clearance of hepatitis B virus (HBV) surface antigen (HBsAg) in HBV‐infected patients who had not received antiviral therapy. The current study evaluated the impact of serum miR‐122 levels on HBsAg seroclearance in 367 consecutive HBV‐infected patients who had not received antiviral therapy between their initial and last visit, and investigated the predictive factors of HBsAg seroclearance. Cumulative HBsAg seroclearance rates were 13.5%, 32.0%, and 37.4% after 10, 20, and 30 years, respectively. The yearly incidence of HBsAg seroclearance over the investigated 30‐year period was 1.25%. A significant and strong correlation was observed between serum miR‐122 and HBsAg levels. Moreover, there was a significant correlation between serum miR‐122 levels and the levels of HBV DNA, hepatitis B e‐antigen, and HBV core‐related antigen. The HBsAg seroclearance rate in patients with a <1.0‐fold change of serum miR‐122 levels was significantly higher than in those with a ≥1.0‐fold change. Multivariate analysis identified age (≥30 years), HBV DNA levels (<2.2 log U/mL), HBV genotype (non‐C), and serum miR‐122 levels (<1.0‐fold change) as significant predictors of HBsAg seroclearance. Our results indicated that serum miR‐122 level is an important predictor of HBsAg seroclearance in Japanese patients who do not receive antiviral therapy. Understanding the complexity of the interactions among various virus‐related and host‐related factors could potentially help in the design of new therapies that enhance HBsAg seroclearance.
Standard and line‐to‐line cementation of a polished short hip stem: Long‐term in vitro implant stability
Authors: Morellato Kavin , Grupp Thomas M. , Bader Uwe , Sungu Mevluet , Fink Bernd , Cristofolini Luca
Published: June 2018

The current trend is toward shorter hip stems. While there is a general agreement on the need for a cement mantle thicker than 2 mm, some surgeons prefer line‐to‐line cementation, where the mantle has only the thickness provided by the cement‐bone interdigitation. The aim of this study was to assess if a relatively short, polished hip stem designed for a standard cementation can also be cemented line‐to‐line without increasing the risk of long‐term loosening. Composite femurs with specific open‐cell foam to allow cement‐bone interdigitation were used. A validated in‐vitro biomechanical cyclic test replicating long‐term physiological loading was applied to femurs where the same stem was implanted with the Standard‐mantle (optimal stem size) and Line‐to‐line (same rasp, one‐size larger stem). Implant‐bone motions were measured during the test. Inducible micromotions never exceeded 10 μm for both implant types (differences statistically not‐significant). Permanent migrations ranged 50–300 μm for both implant types (differences statistically not‐significant). While in the standard‐mantle specimens there was a pronounced trend toward stabilization, line‐to‐line had less tendency to stabilize. The cement cracks were observed after the test by means of dye penetrants: The line‐to‐line specimens included the same cracks of the standard‐mantle (but in the line‐to‐line specimens they were longer), and some additional cracks. The micromotions and cement damage were consistent with those observed in‐vitro and clinically for stable stems, confirming that none of the specimens became dramatically loose. However, it seems that for this relatively short polished stem, standard‐mantle cementation is preferable, as it results in less micromotion and less cement cracking. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2736–2744, 2018.
Improvement of bone‐tendon fixation by porous titanium interference screw: A rabbit animal model
Authors: Tsai Pei‐I , Chen Chih‐Yu , Huang Shu‐Wei , Yang Kuo‐Yi , Lin Tzu‐Hung , Chen San‐Yuan , Sun Jui‐Sheng
Published: June 2018

The interference screw is a widely used fixation device in the anterior cruciate ligament (ACL) reconstruction surgeries. Despite the generally satisfactory results, problems of using interference screws were reported. By using additive manufacturing (AM) technology, we developed an innovative titanium alloy (Ti6Al4V) interference screw with rough surface and inter‐connected porous structure designs to improve the bone‐tendon fixation. An innovative Ti6Al4V interference screws were manufactured by AM technology. In vitro mechanical tests were performed to validate its mechanical properties. Twenty‐seven New Zealand white rabbits were randomly divided into control and AM screw groups for biomechanical analyses and histological analysis at 4, 8, and 12 weeks postoperatively; while micro‐CT analysis was performed at 12 weeks postoperatively. The biomechanical tests showed that the ultimate failure load in the AM interference screw group was significantly higher than that in the control group at all tested periods. These results were also compatible with the findings of micro‐CT and histological analyses. In micro‐CT analysis, the bone‐screw gap was larger in the control group; while for the additive manufactured screw, the screw and bone growth was in close contact. In histological study, the bone‐screw gaps were wider in the control group and were almost invisible in the AM screw group. The innovative AM interference screws with surface roughness and inter‐connected porous architectures demonstrated better bone‐tendon‐implant integration, and resulted in stronger biomechanical characteristics when compared to traditional screws. These advantages can be transferred to future interference screw designs to improve their clinical performance. The AM interference screw could improve graft fixation and eventually result in better biomechanical performance of the bone‐tendon‐screw construct. The innovative AM interference screws can be transferred to future interference screw designs to improve the performance of implants. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2633–2640, 2018.
Microcalorimetric detection of staphylococcal biofilm growth on various prosthetic biomaterials after exposure to daptomycin
Authors: Ravn Christen , Ferreira Inês S. , Maiolo Elena , Overgaard Søren , Trampuz Andrej
Published: June 2018

Primary aim of this in vitro study was to test the efficacy of daptomycin to eradicate staphylococcal biofilms on various orthopedic implant materials. Secondary aim was to quantitatively estimate the formation of staphylococcal biofilm. We tested six clinically important biomaterials: Cobalt chrome, pure titanium, grid‐blasted titanium, porous plasma‐coated titanium with/without hydroxyapatite, and polyethylene. Biofilms of S. aureus and S. epidermidis were formed on the samples and thereafter exposed to daptomycin. Samples were subsequently sonicated in order to detect dislodged biofilm bacteria and transferred to a microcalorimeter for real‐time measurement of growth‐related heat flow. Minimal biofilm eradication concentration (MBEC) was determined as the lowest concentration of daptomycin required to eradicate biofilm bacteria on the sample. Median MBEC of S. aureus biofilm on smooth metallic surfaces was lower than the rough metallic surfaces. In experiments with S. epidermidis, no pattern was seen in relation to the surface roughness. Regarding the quantitative estimation of staphylococcal biofilm formation on the sample, we found a significantly higher amount of biofilm growth on the rough surfaces than the smooth samples and polyethylene. In conclusion, the presented study showed that daptomycin could eradicate S. aureus biofilm at lower concentrations on the smooth surfaces compared to the rough surfaces, as well as polyethylene. In experiments with daptomycin against S. epidermidis biofilms, no pattern was seen in relation to the surface roughness. Furthermore, we demonstrated a faster detection of staphylococcal heat flow due to higher biofilm quantity on the rough surfaces compared to smooth samples and polyethylene. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2809–2816, 2018.
Potential of lactic acid bacteria to modulate coffee volatiles and effect of glucose supplementation: fermentation of green coffee beans and impact of coffee roasting
Authors: Wang Chenhui , Sun Jingcan , Lassabliere Benjamin , Yu Bin , Zhao Feifei , Zhao Fangju , Chen Ying , Liu Shao Quan
Published: June 2018

BACKGROUND

Coffee flavor can be significantly influenced by microbial activities in spontaneous fermentation of coffee cherries. The potential of lactic acid bacteria for flavor modulation through controlled fermentation of green coffee beans has not been explored.

RESULTS

Fermentation by Lactobacillus rhamnosus HN001 with and without 1% w/w glucose supplementation led to modification of flavor‐related constituents in green coffee beans, which translated into modulation of coffee volatiles upon roasting. The lactic acid bacteria consumed almost all glucose and fructose, leaving sucrose behind. Amino acids and malic, citric, and succinic acids were partially catabolized. Glucose supplementation enhanced lactic acid production but repressed acetic acid formation. After roasting at 235 °C for 9 min, 12 min, and 15 min, the levels of furfurals in glucose‐supplemented‐fermented coffee were 10.5‐, 2.7‐, and 1.1‐fold higher than those in the controls (nonsupplemented‐unfermented coffee); furthermore, the levels of pyrazines in the controls were 11.9‐, 10.1‐, and 6.5‐fold higher than those in the treated coffee. Glucose‐supplemented fermentation yielded roasted coffee with stronger caramelic and burnt characteristics but weaker nutty notes. In roasted non‐supplemented‐fermented coffee, volatile production was generally reduced, resulting in a milder overall aroma.

CONCLUSION

Lactic acid fermentation of green coffee beans is a new strategy for coffee flavor modulation, creating novel aroma characteristics. © 2018 Society of Chemical Industry
1H‐NMR‐based water‐soluble low molecular weight compound characterization and fatty acid composition of boiled Wuding chicken during processing
Authors: Xiao Zhichao , Luo Yuting , Wang Guiying , Ge Changrong , Zhou Guanghong , Zhang Wangang , Liao Guozhou
Published: June 2018

BACKGROUND

Boiled Wuding chicken was produced using whole chicken by washing, boiling 1 h with salt, deep frying, and boiling 2 h. The effect of the process on the water‐soluble low molecular weight (WLOM) compound profiles of products was characterized using proton nuclear magnetic resonance spectroscopy, and the fatty acid composition of products was analyzed using gas chromatography–mass spectrometry.

RESULTS

The metabolome was dominated by 49 WLOM compounds, and 22 fatty acid compounds were detected. Principal component (PC)1 and PC2 explained a total of 93.4% and 3% of variance respectively. Compared with the control group, the total WLOM compound and fatty acid contents of the chicken breast were significantly decreased in the other three processing stages (P < 0.05). Comprehensive multivariate data analysis showed significant differences about precursor substance between the different processing including creatine, lactate, creatinine, glucose, taurine, anserine, and acetate (P < 0.05).

CONCLUSION

These results contribute to a more accurate understanding of precursor substance changes of flavor in chicken meat during processing. Boiled, treated chicken had significant effects on fatty acid and WLOM compounds. © 2018 Society of Chemical Industry
The ambident electrophilic behavior of 5‐nitro‐3‐X‐thiophenes in σ‐complexation processes
Authors: Gabsi Wahiba , Essalah Khalid , Goumont Régis , Tangour Bahoueddine , Boubaker Taoufik
Published: June 2018

Kinetics of the reactions of 3,5‐dinitrothiophene 1 and 3‐cyano‐5‐nitrothiophene 2 with a series of parasubstituted phenoxide anions 3a–c have been investigated in aqueous solution at 20°C. Two unsubstituted electrophilic centers (C(2) and C(4)) of the two thiophenes have been identified. The Fukui functions correctly predict the C(2) and C(4) atoms as the most electrophilic centers of these electron‐deficient thiophenes 1 and 2. Analysis of the experimental data in terms of Brønsted relationships reveals that the reaction mechanism likely involves a single‐electron transfer (SET) process. The excellent correlations upon plotting the rate constants versus the oxidation potentials Eo values is an additional evidence that reactions between thiophenes and phenoxide anions are proceeding through an initial electron transfer. It is of particular interest to note that the systems studied in this paper provide a rare example of a SET mechanism in σ‐complexation reactions. According to the free energy relationship log k = s(N + E) (Angew. Chem., Int. Ed. Engl., 1994, 33, 938–957), the electrophilicity parameters E of the C‐4 and C‐2 positions of the thiophenes have been determined and compared with the reactivities of other ambident electrophiles. On the other hand, the second‐order rate constants for the reactions of these thiophenes with the hydroxide ion has been measured in water and 50% water–50% acetonitrile and found to agree with those calculated theoretically using Mayr's equation from the E values determined in this work and from the previously published N and s parameters of OH−.
Isothiocyanates from Brassica Vegetables—Effects of Processing, Cooking, Mastication, and Digestion
Authors: Oliviero Teresa , Verkerk Ruud , Dekker Matthijs
Published: June 2018

The formation of health‐beneficial isothiocyanates (ITCs) from glucosinolates depends on a wide variety of plant‐intrinsic factors (e.g., concentration of glucosinolates, activity of myrosinase, and specifier proteins) and on a multitude of extrinsic postharvest factors such as the conditions used during industrial processing, domestic preparation, mastication, and digestion. All of these factors contribute to a large variability in the formation of ITCs (and other breakdown products), as well as their intake and absorption upon consumption of Brassica vegetables. This uncertainty in ITC intake and absorption is a barrier for the determination of an optimal Brassica vegetable consumption pattern. In this review, the intrinsic and extrinsic factors that affect the formation, intake, and absorption of ITCs are described according to the most recent findings. The focus of this review includes the hydrolysis reaction mechanisms, the elucidation of the primary factors that play a role in the hydrolysis reaction, the influence of processing and cooking conditions, the effect of chewing, and the roles of the gastric and upper intestinal phases, including the effect of the meal composition (e.g., the effect of other meal compounds present during digestion) on the potential formation of ITCs.
Organ doses in pediatric patients undergoing cardiac‐centered fluoroscopically guided interventions: Comparison of three methods for computational phantom alignment
Authors: Marshall Emily L. , Borrego David , Fudge James C. , Rajderkar Dhanashree , Bolch Wesley E.
Published: June 2018

Purpose

To assess various computational phantom alignment techniques within Monte Carlo radiation transport models of pediatric fluoroscopically guided cardiac interventional studies.

Methods

Logfiles, including all procedure radiation and machine data, were extracted from a Toshiba infinix‐I unit in the University of Florida Pediatric Catheterization Laboratory for a cohort of 10 patients. Two different alignment methods were then tested against a ground truth standard based upon identification of a unique anatomic reference point within images co‐registered to specific irradiation events within each procedure. The first alignment method required measurement of the distance from the edge of the exam table to the top of the patient's head (table alignment method). The second alignment method fixed the anatomic reference point to be the geometric center of the heart muscle, as all 10 studies were cardiac in nature. Monte Carlo radiation transport simulations were performed for each patient and intervention using morphometry‐matched hybrid computational phantoms for the reference and two tested alignment methods. For each combination, absorbed doses were computed for 28 organs and root mean square organ doses were assessed and compared across the alignment methods.

Results

The percent error in root mean square organ dose ranged from −57% to +41% for the table alignment method, and from −27% to +22% for the heart geometric centroid alignment method. Absorbed doses to specific organs, such as the heart and lungs, demonstrated higher accuracy in the heart geometric centroid alignment method, with average percent errors of 10% and 1.4%, respectively, compared to average percent errors of −32% and 24%, respectively, using the table alignment method.

Conclusions

Of the two phantom alignment methods investigated in this study, the use of an anatomical reference point — in this case the geometric centroid of the heart — provided a reliable method for radiation transport simulations of organ dose in pediatric interventional cardiac studies. This alignment method provides the added benefit of requiring no physician input, making retrospective calculations possible. Moving forward, additional anatomical reference methods can be tested to assess the reliability of anatomical reference points beyond cardiac centered procedures.
Establishing action threshold for change in patient anatomy using EPID gamma analysis and PTV coverage for head and neck radiotherapy treatment
Authors: Piron Ophélie , Varfalvy Nicolas , Archambault Louis
Published: June 2018

Purpose

To present a new adaptive radiotherapy (ART) method based on relative gamma analysis and patient classification for the identification of anatomical changes that induce a sufficient dosimetric impact to affect the treatment delivery and require complete replanning.

Methods

This retrospective study includes 55 patients treated for a head and neck cancer with IMRT, VMAT, or 3D conformal RT. Electronic Portal Imaging Device images for all treatment fields were acquired daily at every fraction. CBCTs were collected at least once a week. Gamma analysis was performed using the first fraction of the treatment as a reference once validated that it was delivered without error. Gamma analysis parameters (<γ>, standard deviation and the Top 1% γ) were used to define categories using statistic from a k‐means clustering analysis. From these categories an action threshold was defined and correlated with dosimetric changes. For 23 of 55 patients, the V100% for PTV was computed for both, the planning CT and original contours deformed onto CBCT acquired at the last fraction. These values were then compared with 2D image relative γ‐analysis of EPID images. Sensitivity and specificity of the method for the detection of dosimetric changes were computed.

Results

Three categories indicating an increasing level of change with the planned treatment were identified. A threshold was established for which patients were at risk of deviation at <γ> = 0.42. From 23 recomputing plans, it has been confirmed that patients with a strong dosimetric impact were above this threshold, with a specificity of 0.80 and a sensitivity of 0.84.

Conclusions

The specificity and the sensitivity value confirmed the performance of the method to detect anatomical changes. The γ‐analysis threshold correlated well with morphological changes that have a relevant dosimetric impact. Analysis of daily EPID images provides a method to identify patients at risk of deviation from their planned treatment and can support an early replanning decision.
Technical Note: Extension of CERR for computational radiomics: A comprehensive MATLAB platform for reproducible radiomics research
Authors: Apte Aditya P. , Iyer Aditi , Crispin‐Ortuzar Mireia , Pandya Rutu , van Dijk Lisanne V. , Spezi Emiliano , Thor Maria , Um Hyemin , Veeraraghavan Harini , Oh Jung Hun , Shukla‐Dave Amita , Deasy Joseph O.
Published: June 2018

Purpose

Radiomics is a growing field of image quantitation, but it lacks stable and high‐quality software systems. We extended the capabilities of the Computational Environment for Radiological Research (CERR) to create a comprehensive, open‐source, MATLAB‐based software platform with an emphasis on reproducibility, speed, and clinical integration of radiomics research.

Method

The radiomics tools in CERR were designed specifically to quantitate medical images in combination with CERR's core functionalities of radiological data import, transformation, management, image segmentation, and visualization. CERR allows for batch calculation and visualization of radiomics features, and provides a user‐friendly data structure for radiomics metadata. All radiomics computations are vectorized for speed. Additionally, a test suite is provided for reconstruction and comparison with radiomics features computed using other software platforms such as the Insight Toolkit (ITK) and PyRadiomics. CERR was evaluated according to the standards defined by the Image Biomarker Standardization Initiative. CERR's radiomics feature calculation was integrated with the clinically used MIM software using its MATLAB® application programming interface.

Results

The CERR provides a comprehensive computational platform for radiomics analysis. Matrix formulations for the compute‐intensive Haralick texture resulted in speeds that are superior to the implementation in ITK 4.12. For an image discretized into 32 bins, CERR achieved a speedup of 3.5 times over ITK. The CERR test suite enabled the successful identification of programming errors as well as genuine differences in radiomics definitions and calculations across the software packages tested.

Conclusion

The CERR's radiomics capabilities are comprehensive, open‐source, and fast, making it an attractive platform for developing and exploring radiomics signatures across institutions. The ability to both choose from a wide variety of radiomics implementations and to integrate with a clinical workflow makes CERR useful for retrospective as well as prospective research analyses.
Least‐square collocation and Lagrange multipliers forTaylor meshless method
Authors: Yang Jie , Hu Heng , Potier‐Ferry Michel
Published: June 2018

A recently proposed meshless method is discussed in this article. It relies on Taylor series, the shape functions being high degree polynomials deduced from the Partial Differential Equation (PDE). In this framework, an efficient technique to couple several polynomial approximations has been presented in (Tampango, Potier‐Ferry, Koutsawa, Tiem, Int. J. Numer. Meth. Eng. vol. 95 (2013) pp. 1094–1112): the boundary conditions were applied using the least‐square collocation and the interface was coupled by a bridging technique based on Lagrange multipliers. In this article, least‐square collocation and Lagrange multipliers are applied for boundary conditions, respectively, and least‐square collocation is revisited to account for the interface conditions in piecewise resolutions. Various combinations of these two techniques have been investigated and the numerical results prove their effectiveness to obtain very accurate solutions, even for large scale problems.
A mixed hp FEM for the approximation of fourth‐order singularly perturbed problems on smooth domains
Authors: Constantinou P. , Franz S. , Ludwig L. , Xenophontos C.
Published: June 2018

We consider fourth‐order singularly perturbed problems posed on smooth domains and the approximation of their solution by a mixed Finite Element Method on the so‐called Spectral Boundary Layer Mesh. We show that the method converges uniformly, with respect to the singular perturbation parameter, at an exponential rate when the error is measured in the energy norm. Numerical examples illustrate our theoretical findings.
A Cauchy integral method of the solution of the 2D Dirichlet problem for simply or doubly connected domains
Authors: Shirokova Elena A. , El‐Shenawy Atallah
Published: June 2018

In this paper we propose a new method for solving the 2D Laplace equation with Dirichlet boundary conditions in simply and doubly connected domains. Here, we apply the numerical algorithm based on truncated Fourier series and reduce the corresponding Fredholm integral equation to a finite system of linear equations.
Image Simulation and Analysis
Authors: Sengebusch Karsten
Published: June 2018

No image is perfect, except for paintings.

We have to deal with various noise sources and image sensor artifacts as well as with diffraction and other geometrical effects. The simulation of such artifacts is a great help during a design process and a perfect method for proof of concepts: Without access to any real hardware it is possible to predict and visualize the performance of opto‐electronic systems.

Algorithms for correction or analysis of image data can be developed and evaluated a long time before the imaging hardware is ready to use. The statistical methods used during the simulation process can also be used reversely to provide a deep statistical analysis of already existing images. Such an analysis as well as the comparison with simulated images can help to identify the source of artifacts and design mistakes or even be used during forensic work.

Last but not least, the reverse usage of the simulation of diffraction and wave front propagation is a very effective method for the generation of computer generated holograms or DOEs.
Measuring Thin Transparent Films Precisely
Authors: Quinten Michael
Published: June 2018

The determination of the thickness of thin transparent films with reflectometry is a well‐established cost‐effective robust method that can be used even in inline measurements. The method is based on measurements of the reflectance of the film and a numerical evaluation of the reflectance either by fast Fourier transform or nonlinear regression. In both cases the significance of the result depends upon several parameters in the used algorithms. We demonstrate how reliable the obtained thickness values are.
Let There Be Structured Light
Authors: Park Georgina , Ritchey Carey , Siddall Joe
Published: June 2018

Automated optical inspection (AOI) is a powerful technique used in many manufacturing settings to provide real‐time, decisive measurements related to part quality. AOI is a great tool for the analysis of product defects, from simple mechanical errors to more complex failure mechanisms. Identifying defective parts early in the line, and either reworking them or rejecting them, can save companies money and help build a stronger product‐quality reputation.
New Illumination Technology for Mask Aligner Lithography
Authors: Paster Martin , Weichelt Tina
Published: June 2018

Nowadays, integrated semiconductor circuits are used as components in nearly every electrical device. This would be difficult to imagine without the application of photolithography, one of the essential manufacturing methods in semiconductor and microsystem technology. In a German research project run by the Friedrich Schiller University Jena in collaboration with the Fraunhofer IOF, the conventionally used mercury vapor lamp for mask aligner lithography has been replaced by a laser from the manufacturer InnoLas Photonics and has opened completely new perspectives.
Metal allergy as a late‐onset complication of the Nuss procedure in a pediatric patient
Authors: Navratil Marta , Batinica Maja , Ivković‐Jureković Irena
Published: June 2018

We report the case of a 14‐year‐old boy with pectus excavatum who developed a metal allergy to stainless steel bar as a late‐onset complication after the Nuss procedure. He did not have atopic diathesis. Treatment with oral steroids was effective and the metal bar was successfully removed 2 years later.