bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and modularized optimization of one‐step production of N‐acetylneuraminic acid from chitin in Serratia marcescens
Authors: Yan Qiang , Fong Stephen S. 
Published: June 2018

AbstractChitin is an abundant, biorenewable, nitrogen‐rich biomass feedstock that can be potentially developed for biochemical production; however, efficient bioprocesses have yet to be established. Here, we demonstrate an engineered bioprocess to produce N‐acetylneuraminic acid (Neu5Ac) directly from chitin using the chitinolytic bacterium, Serratia marcescens by selecting and characterizing promoters, characterization of heterologous enzyme activity, and optimization of pathway fluxes. By generating RNASeq data for S. marcescens growth in different carbon‐limited conditions (glucose, N‐acetylglucosamine, and glycerol), 12 promoters with varying strength were identified and characterized to implement for transcriptional control. Neu5Ac production was initially engineered into S. marcescens through heterologous expression of N‐acetylglucosamine 2‐epimerase (slr1975) and N‐acetylneuraminic acid aldolase (nanA). The activity of both genes was characterized in vitro for kinetics and in vivo expression using promoters identified in this study. Optimization of Neu5Ac production was accomplished by balancing pathways fluxes through promoter swapping and replacing the reversible nanA with the irreversible gene neuB. The optimized recombinant strain P
T5‐slr1975‐P
rplJ‐neuB was able to produce 0.48 g/L Neu5Ac from 20 g/L N‐acetylglucosamine, and 0.30 g/L Neu5Ac from 5 g/L crystal chitin. These results represent the first demonstration of direct conversion of crystal chitin to N‐acetylneuraminic acid.
Outline‐etching image segmentation reveals enhanced cell chirality through intercellular alignment
Authors: Huang Yaozhun , Bao Yuanye , Kwong Hoi Kwan , Chen Ting‐Hsuan , Lam Miu Ling 
Published: June 2018

AbstractCells cultured on micropatterns exhibit a chiral orientation, which may underlie the development of left–right asymmetry in tissue microarchitectures. To investigate this phenomenon, fluorescence staining of nuclei has been used to reveal such orientation. However, for images with high cell density, analysis is difficult because of the overlapping nuclei. Here, we report an image processing method that can acquire cell orientations within dense cell populations. After initial separation based on Boolean addition of binarized images using global and adaptive thresholds, the overlapping nucleus contours in the binarized images were segmented by iteratively etching the outlines of nuclei, which allowed the orientations of each cell to be extracted from densely packed cell clusters. In applying this technique to cultured C2C12 myoblasts in micropatterned stripes on different substrates, we found an enhanced chiral orientation on glass substrate. More important, this enhanced chirality was consistently observed with increased intercellular alignment and independent of cell–cell distance or cell density, suggesting that intercellular alignment plays a role in determining the chiral orientation. By segmenting single cells with intact orientation, this technique offers an automated method for quantitative analysis with improved accuracy, providing an essential tool for studying left–right asymmetry and other morphogenic dynamics in tissue formation.
River response to large‐dam removal in a Mediterranean hydroclimatic setting: Carmel River, California, USA
Authors: Harrison Lee R. , East Amy E. , Smith Douglas P. , Logan Joshua B. , Bond Rosealea M. , Nicol Colin L. , Williams Thomas H. , Boughton David A. , Chow Kaitlyn , Luna Lauren 
Published: June 2018

AbstractDam removal provides a valuable opportunity to measure the fluvial response to changes in both sediment supply and the processes that shape channel morphology. We present the first study of river response to the removal of a large (32‐m‐high) dam in a Mediterranean hydroclimatic setting, on the Carmel River, coastal California, USA. This before‐after/control‐impact study measured changes in channel topography, grain size, and salmonid spawning habitat throughout dam removal and subsequent major floods. During dam removal, the river course was re‐routed in order to leave most of the impounded sediment sequestered in the former reservoir and thus prevent major channel and floodplain aggradation downstream. However, a substantial sediment pulse occurred in response to base‐level fall, knickpoint migration, and channel avulsion through sediment in the former reservoir above the newly re‐routed channel. The sediment pulse advanced ~3.5 km in the first wet season after dam removal, resulting in decreased riverbed grain size downstream of the dam site. In the second wet season after dam removal, high flows (including a 30‐year flood and two 10‐year floods) transported sediment > 30 km downstream, filling pools and reducing cross‐channel relief. Deposition of gravel in the second wet season after dam removal enhanced salmonid spawning habitat downstream of the dam site. We infer that in dam removals where most reservoir sediment remains impounded and where high flows follow soon after dam removal, flow sequencing becomes a more important driver of geomorphic and fish‐habitat change than the dam removal alone. © 2018 John Wiley & Sons, Ltd.
Cover Image, Volume 93, Issue 8
Authors: Delgove Marie AF , Elford Matthew T , Bernaerts Katrien V , De Wildeman Stefaan MA 
Published: July 2018

The cover image, by Marie AF Delgove et al., is based on the Research Article Application of a thermostable Baeyer–Villiger monooxygenase for the synthesis of branched polyester precursors, DOI: 10.1002/jctb.5623.
image
Greater Nutrient Intake Is Associated With Lower Mortality in Western and Eastern Critically Ill Patients With Low BMI: A Multicenter, Multinational Observational Study
Authors: Compher Charlene , Chittams Jesse , Sammarco Therese , Higashibeppu Naoki , Higashiguchi Takashi , Heyland Daren K. 
Published: June 2018

AbstractBackground: Little is known about the impact of feeding adequacy by NUTrition Risk in the Critically Ill (NUTRIC) groups in critically ill patients with body mass index (BMI) <20. Our purpose was to assess whether adequacy of protein/energy intake impacts mortality in patients with BMI <20 in Western/Eastern intensive care units (ICUs) and high/low NUTRIC groups.Methods: Data from the International Nutrition Survey 2013–2014 were dichotomized into Western/Eastern ICU settings; BMI <20 or ≥20; and high (≥5)/low (<5) NUTRIC groups. Association of BMI <20 with 60‐day mortality was compared in unadjusted and adjusted (Western/Eastern, age, medical/surgical admission, high/low NUTRIC group) logistic regression models. The impact of adequacy of protein/energy on 60‐day mortality relationship was tested using general estimating equations in high/low NUTRIC groups, in unadjusted and adjusted models.Results: Western (n = 4274) patients had higher mean BMI (27.9 ± 7.7 versus (vs) 23.4 ± 4.9,P< 0.0001) than Eastern (n = 1375), respectively. BMI <20 was associated with greater mortality (adjusted odds ratio [OR] 1.30, 95% confidence interval [CI] 1.07–1.57), with no interaction between BMI group and Western/Eastern ICU site. Among patients with BMI <20 and high NUTRIC score, 10% greater protein and energy adequacy was associated with 5.7% and 5.5% reduction in 60‐day mortality, respectively. Results were not significantly different between Western and Eastern ICUs.Conclusions: The benefit of greater protein/energy intake in high‐NUTRIC patients was observed regardless of geographic origin or low BMI, suggesting a consistent response to nutrition support in this group. Clinical guidelines and research projects focused on improving care in high‐risk critically ill patients can be applied across geographic boundaries.
Enteral Protein Supplementation in Critically Ill Children: A Randomized Controlled Pilot and Feasibility Study
Authors: Hauschild Daniela B. , Oliveira Luna D. A. , Farias Mirelle S. , Barbosa Eliana , Bresolin Nilzete L. , Mehta Nilesh M. , Moreno Yara M. F. 
Published: June 2018

AbstractBackgroundLoss of muscle mass in critically ill children can negatively impact outcomes. The aims of this study were to conduct a pilot randomized control trial (RCT) to examine the difference in protein delivery and nitrogen balance in critically ill children with enteral protein supplementation vs controls. We also aimed to assess the feasibility, safety, and tolerance of the pilot trial.MethodsThis is a 3‐arm RCT in critically ill children eligible for enteral nutrition (EN) therapy. Patients were randomized to 1 of the 3 groups: (1) control (routine EN), (2) polymeric protein module added to EN to reach protein goal by day 4, or (3) oligomeric protein supplementation. Demographics, clinical characteristics, nutrition status, and daily nutrition intake variables were recorded. Protein delivery, nitrogen balance, feasibility variables, and rate of adverse events were the outcomes.ResultsAfter screening 286 consecutive patients admitted to the pediatric intensive care unit over 11 months, we enrolled and randomized 25 patients. Twenty‐two patients (88% of the enrolled) completed the study procedures. Significantly higher protein prescription and actual protein intake within the first 5 days was achieved in the intervention groups, compared with the control group. Nitrogen balance was obtained in 15 patients. There was no significant difference between the groups for the rate of adverse effects and clinical outcomes.ConclusionIn our pilot trial, protein supplementation was safe and well tolerated. Our preliminary results suggest that a larger RCT is potentially feasible, with some modifications of the entry criteria. Trial enrollment was low, likely due to restrictive entry criteria.
Correction of severe beam‐hardening artifacts via a high‐order linearization function using a prior‐image‐based parameter selection method
Authors: Oh Daejoong , Kim Sewon , Park Doohyun , Choi Seungwon , Song Hundong , Choi Yunsu , Moon Seunghyuk , Baek Jongduk , Hwang Dosik 
Published: June 2018

PurposePolychromatic x‐rays are used in most computed tomography scanners. In this case, a beam‐hardening effect occurs, which degrades the image quality and distorts the shapes of objects in the reconstructed images. When the beam‐hardening artifact is not severe, conventional correction methods can reduce the artifact reasonably well. However, highly dense materials, such as iron and titanium, can produce more severe beam‐hardening artifacts, which often cannot be corrected by conventional methods. Moreover, when the size of the metal is large, severe darks bands due to photon starvation as well as beam‐hardening are generated. The purpose of our study was to develop a new method for correcting severe beam‐hardening artifacts and severe dark bands using a high‐order polynomial correction function and a prior‐image‐based linearization method.MethodsThe initial estimate of an image free of beam‐hardening (a prior image) was constructed from the initial reconstruction of the original projection data. Its corresponding beam‐hardening‐free projection data (a prior projection) were calculated by a projection operator onto the prior image. A new beam‐hardening correction function G(praw) with many high‐order terms was effectively determined via a simple minimization process applied to the difference between the original projection data and the prior projection data. Using the determined correction function G(praw), a corrected linearized sinogram pcorr can be obtained, which became effectively linear for the line integrals of the object. Final beam‐hardening corrected images can be reconstructed from the linearized sinogram. The proposed method was evaluated in both simulation and real experimental studies.ResultsAll investigated cases in both simulations and real experiments showed that the proposed method effectively removed not only streaks for moderate beam‐hardening artifacts but also dark bands for severe beam‐hardening artifacts without causing structural and contrast distortion.ConclusionsThe prior‐image‐based linearization method exhibited better correction performance than conventional methods. Because the proposed method did not require time‐consuming iterative reconstruction processes to obtain the optimal correction function, it can expedite the correction procedure and incorporate more high‐order terms in the linearization correction function in comparison to the conventional methods.
Performance characterization of an integrated cone‐beam CT system for dedicated gamma radiosurgery
Authors: Sarfehnia Arman , Ruschin Mark , Chugh Brige , Yeboah Collins , Becker Nathan , Cho Young‐Bin , Lee Young 
Published: June 2018

PurposeThis work describes the performance characterization of a cone‐beam CT‐guided radiosurgery device, the Gamma Knife® Icon™.MethodsThe performance tests have been categorized into: (a) image quality and mechanical integrity; (b) image coregistration fidelity; (c) adaptive treatment delivery quality; (d) high definition motion management performance characterization; (e) software communication performance testing of the integrated cone‐beam CT (CBCT) system.ResultsAll image quality performance characterization satisfied or exceeded manufacturer specifications. The image quality and mechanical stability of the CBCT system over a 3‐month period was within tolerance with negligible (<0.1°) detector tilt angle. The CBCT definition of the stereotactic space had a measured average discrepancy of 0.15–0.16 mm in x, y, and z directions. On average, the high definition motion management system performance was within 0.05 mm with a residual offset of 0.15 mm when large displacements in a given direction were taken. The adaptive treatment delivery component as measured with CBCT coregistration of daily setups against reference setup images was accurate to within 0.2°. Comprehensive end‐to‐end testing showed a total uncertainty of better than 0.2 mm in positioning and 0.4% in dosimetry for treatment of centrally located lesions.ConclusionsA set of system performance characterization tests spanning all aspects of the Gamma Knife Icon are presented. Overall, the system performance was in line with manufacturer specifications.
Comparison of Two Methods for Estimating the Tip Position of a Nasogastric Feeding Tube: A Randomized Controlled Trial
Authors: Torsy Tim , Saman Renée , Boeykens Kurt , Duysburgh Ivo , Van Damme Nele , Beeckman Dimitri 
Published: June 2018

AbstractBackgroundSeveral studies have shown that the nose‐earlobe‐xiphoid distance (NEX) is inadequate to estimate the insertion length of nasogastric tubes. An alternative approach tested in these studies, which leads to > 90% well‐placed nasogastric tubes, used a corrected calculation of the NEX: (NEX × 0.38696) + 30.37. The primary aim of this study was to determine whether using the corrected NEX was more successful than the NEX in determining the insertion length. The secondary aim was to investigate the likelihood to successfully obtain gastric aspirate.MethodsAdult patients in a general hospital (N = 215) needing a nasogastric tube were randomized to the control (NEX) or intervention group (corrected NEX). Tip positioning was verified using X‐ray. Correct tip positioning was defined as between 3 and 10 cm under the lower esophageal sphincter (LES).ResultsIn >20% of all patients, both methods underestimated the required tube length for correct positioning. The NEX showed an overestimation (17.2%) of the insertion length (>10 cm under the LES) compared with the corrected NEX (4.8%). There was no difference (P = 0.938) between the 2 groups in obtaining gastric aspirate (55.6% vs 56%). However, correct tip positioning resulted in a fourfold increase of obtaining gastric aspirate.ConclusionsBoth methods resulted in a high risk of incorrectly placed tubes due to malposition of the tip near the LES or distal esophagus. This may increase the risk of reflux and pulmonary aspiration. Based on these results, the development of more reliable methods requires consideration.
Reward‐enhancing effect of methylphenidate is abolished in dopamine transporter knockout mice: A model of attention‐deficit/hyperactivity disorder
Authors: Ide Soichiro , Ikekubo Yuiko , Hua Jennifer , Takamatsu Yukio , Uhl George R. , Sora Ichiro , Ikeda Kazutaka 
Published: June 2018

AbstractAimAttention‐deficit/hyperactivity disorder is a heterogeneous neurobiological disorder that is characterized by inattention, impulsivity, and an increase in motor activity. Although methylphenidate has been used as a medication for decades, unknown is whether methylphenidate treatment can cause drug dependence in patients with attention‐deficit/hyperactivity disorder. This study investigated the reward‐enhancing effects of methylphenidate using intracranial self‐stimulation in an animal model of attention‐deficit/hyperactivity disorder, dopamine transporter knockout mice.MethodsFor the intracranial self‐stimulation procedures, the mice were trained to nosepoke to receive direct electrical stimulation via an electrode that was implanted in the lateral hypothalamus. After the acquisition of nosepoke responding for intracranial self‐stimulation, the effects of methylphenidate on intracranial self‐stimulation were investigated.ResultsIn the progressive‐ratio procedure, dopamine transporter knockout mice exhibited an increase in intracranial self‐stimulation compared with wild‐type mice. Treatment with 5 and 10 mg/kg methylphenidate increased intracranial self‐stimulation responding in wild‐type mice. Methylphenidate at the same doses did not affect intracranial self‐stimulation responding in dopamine transporter knockout mice. We then investigated the effects of high‐dose methylphenidate (60 mg/kg) in a rate‐frequency procedure. High‐dose methylphenidate significantly decreased intracranial self‐stimulation responding in both wild‐type and dopamine transporter knockout mice.ConclusionsThese results suggest that low‐dose methylphenidate alters the reward system (ie, increases intracranial self‐stimulation responding) in wild‐type mice via dopamine transporter inhibition, whereas dopamine transporter knockout mice do not exhibit such alterations. High‐dose methylphenidate appears to suppress intracranial self‐stimulation responding not through dopamine transporter inhibition but rather through other mechanisms. These results support the possibility that methylphenidate treatment for attention‐deficit/hyperactivity disorder does not increase the risk of drug dependence, in attention‐deficit/hyperactivity disorder patients with dopamine transporter dysfunction.
Health literacy and the health status of men with prostate cancer
Authors: Goodwin Belinda C. , March Sonja , Zajdlewicz Leah , Osborne Richard H. , Dunn Jeff , Chambers Suzanne K. 
Published: June 2018

AbstractObjectiveTo test the Health Literacy Questionnaire (HLQ) in a sample of men with prostate cancer and examine the components of health literacy that are most strongly associated with mental and physical health‐related quality of life in men with prostate cancer.MethodMembers (N = 565) of a state‐wide prostate cancer support network in Queensland, Australia (Mage = 71.14, SD = 8.68) completed the HLQ along with the Medical Outcomes Study, 36‐item short‐form health survey (SF‐36). Confirmatory factor analysis was employed to assess the internal structure of the HLQ. The effects (bs) of each of the nine health literacy factors on mental and physical health status were graphed and compared using Fishers exact test for comparing parameter estimates.ResultsFit indices including RMSEA (0.069, CI = 0.066‐0.072), CFI (.853), and TLI (.839), alongside item loadings and internal consistency (Cronbach alphas >0.80) for the nine‐factor model, supported the robustness of the HLQ for use in this prostate cancer sample. Health literacy factors reflecting social and health provider support, navigating health systems, finding and understanding health information, and active engagement with providers shared small to moderate associations with mental health status and little to no association with physical health status.ConclusionFindings provide support for the use of the HLQ as a valid and reliable measure of health literacy in men with prostate cancer. Although further research is required to establish causality, interventions that aim to improve skills in connecting and effectively communicating with health care services and providers might lead to better mental health related quality of life for men with prostate cancer.
Characteristics of colliding density currents: A numerical and theoretical study
Authors: Cafaro Carlo , Rooney Gabriel G. 
Published: June 2018

This paper presents a new set of numerical simulations of two colliding density currents in a idealized framework, integrating the Boussinesq vorticity equation in a rectangular bounded domain. These simulations are used to examine the dynamical features of the collision, in the light of recent laboratory experiments. The collision dynamics present various interesting features. Here we have focused on the interface slope at the front of the two unequal density currents and on the maximum height reached by the fluid after the collision. For the secondary triggering of atmospheric convection by colliding cold pools from previous convective events, these may affect the positioning and the momentum of the collision uplift, respectively.The interface slope has been shown to be dependent on the currents' buoyancy ratio (i.e. the ratio between the density differences of the two fluids with the ambient fluid), whereas the maximum height has no strong dependence, for a given initial current depth. A theoretical model, based on an analogy with a vortex pair, has been proposed for the interface‐slope dependence, taking as input the buoyancy ratio or the propagating speeds. This model agrees reasonably well with the observed numerical values.
Adult rat morphine exposure changes morphine preference, anxiety, and the brain expression of dopamine receptors in male offspring
Authors: Vousooghi Nasim , Sadat‐Shirazi Mitra‐Sadat , Safavi Payam , Zeraati Ramin , Akbarabadi Ardeshir , Makki Seyed Mohammad , Nazari Shahrzad , Zarrindast Mohammad Reza 
Published: June 2018

AbstractAddiction to drugs, including opioids is the result of an interplay between environmental and genetic factors. It has been shown that the progeny of addict people is at higher risk for drug addiction. However, the mechanisms of such trans‐generational effects of drugs are not so clear. Here we have evaluated the effects of parental morphine consumption on anxiety, morphine preference, and mRNA expression of dopamine receptors in F1 and F2 male offspring. Morphine was chronically administered to adult male and female Wistar rats followed by 14‐day abstinence before mating. Morphine preference and anxiety‐like behavior in the offspring were measured by two‐bottle‐choice paradigm and elevated‐plus maze, respectively. Real‐time PCR was used to measure the mRNA expression level of dopamine receptors in the striatum, nucleus accumbens, prefrontal cortex, and hippocampus of F1 animals. The results indicated that F1 but not the F2 male progeny of morphine‐exposed parents had a greater preference for morphine, and more anxiety‐like behavior compared to the offspring of saline‐treated parents. In F1 male progeny of morphine‐treated parents, D1 and D5 dopamine receptors were significantly increased in the prefrontal cortex and nucleus accumbens. D5 and D2 receptors were decreased in the hippocampus. D4 dopamine receptor was augmented in striatum and hippocampus and decreased in the prefrontal cortex. Adulthood exposure to chronic morphine in male and female rats before conception leads to higher morphine preference and increased anxiety in F1 but not F2 male progeny. Alterations of dopamine receptor expression in the reward system may be one mechanism responsible for observed changes in F1 offspring.