bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bamboo biochar does not affect paddy soil N2O emissions or source following slurry or mineral fertilizer amendment—a15N tracer study
Authors: Case Sean D. C. , Uno Hikaru , Nakajima Yasuhiro , Stoumann Jensen Lars , Akiyama Hiroko 
Published: May 2017

AbstractNitrogen (N)‐containing fertilizers, such as slurry and ammonium nitrate (NH4NO3), can significantly increase soil nitrous oxide (N2O) emissions following addition to agricultural soil. Biochar amendment to soil has been observed to suppress N2O emissions in a number of studies. However, the effect varies depending on many factors, including when biochar is added to soil concurrently with organic or mineral fertilizers. An incubation was conducted in which bamboo biochar (created at 800°C) was added to an ex‐rice paddy soil (1% rate) concurrently with dairy cattle slurry or NH4NO3(100 mg N kg−1). At three time points, following biochar amendment,15N‐labelled NH4NO3(50 mg N kg−1) was added to the soil to determine the N2O emissions derived from nitrification and denitrification in the 24 h that followed (at 70% water filled pore space; days 0, 7, and 28). Nitrous oxide emissions from slurry‐amended soils were much greater than those from NH4NO3‐amended soils, as well as the proportion of soil N2O emissions derived from denitrification. Biochar amendment did not significantly affect soil N2O emissions or consistently affect the percentage of soil N2O emissions derived from nitrification in slurry or NH4NO3‐amended treatments. The lack of N2O‐emission suppression with biochar amendment may have been due to the relatively‐low addition rate of a biochar that had a low content of volatile organic carbons and redox‐reactive organic/inorganic compounds, and did not greatly increase the pH of the acidic soil (pH 5). These results suggest that bamboo biochar produced at such a high temperature may not be suitable for mitigation of soil N2O emissions.
Invasive invertebrate predator, Bythotrephes longimanus, reverses trophic cascade in a north‐temperate lake
Authors: Walsh Jake R. , Lathrop Richard C. , Vander Zanden M. Jake 
Published: May 2017

AbstractTrophic cascades can determine the structure of aquatic food webs, a role often used to manage water quality in lakes. However, trophic cascades are subject to multiple interacting drivers of environmental change. For example, invasive species can dramatically alter food webs, though we know less about invasive species effects on managed trophic cascades. Here, we investigate the changing food web dynamics of Lake Mendota (Wisconsin, U.S.A.) over a 40‐yr time period. Piscivore stocking (biomanipulation) beginning in 1988 coupled with a 1987 die‐off of cisco (the dominant zooplanktivore) led to decreased zooplanktivory that cascaded to increases in the large‐bodied herbivorous zooplankton Daphnia pulicaria and greater water clarity. In 2009, the invasive spiny water flea Bythotrephes longimanus was first detected in Lake Mendota and soon reached record densities. As a result of this invasive invertebrate predator, zooplanktivory increased to 47% of the earlier cisco period. Concomitant with the spiny water flea population explosion were declines in D. pulicaria and water clarity as both exhibited a strong negative relationship to zooplanktivory across the 40‐yr time series. We argue that the trophic cascade of 1987–1988 created an environment of high food resources and low fish planktivory that promoted the proliferation of Bythotrephes as it functionally replaced cisco in Lake Mendota's food web. Our results highlight how a manipulated, eutrophic lake was vulnerable to adverse impacts by invasive species, calling attention to the importance of understanding interactions among drivers of environmental change.
Determination of glycolic acid in natural seawater by liquid chromatography coupled with triple quadrupole mass spectrometry
Authors: Hong Haizheng , Li Weiying , Li Xiaolin , Huang Bangqin , Shi Dalin 
Published: May 2017

AbstractGlycolic acid, which is produced during photorespiration, is one of the major components of dissolved organic matter released by phytoplankton, comprising up to 40% of their daily primary productivity. However, the sensitivity of existing methods does not allow for accurate measurement of glycolic acid levels in oligotrophic seawater. In this study, we present a straightforward, robust, and sensitive liquid chromatography‐mass spectrometry (LC‐MS) method to quantify glycolic acid in natural seawater following liquid‐liquid extraction, requiring only a small sample size (25 mL seawater). The method has a highly sensitive detection limit of 9 nM, at least fivefold lower than existing methods. This approach was successfully applied to the analysis of seawater samples collected from both eutrophic and oligotrophic marine environments. The results showed that glycolic acid concentrations in natural seawater are positively correlated with chlorophyll a concentrations, indicating that phytoplankton contribute significantly to glycolic acid production in marine environments. As glycolic acid is an important carbon and energy source for marine bacteria, the method developed within this study allows further investigation into the rates of its release and uptake by phytoplankton and heterotrophic bacteria, respectively, as well as the role it plays in phytoplankton–bacteria interactions.
Self‐Healing Gelatin Hydrogels Cross‐Linked by Combining Multiple Hydrogen Bonding and Ionic Coordination
Authors: Zhang Guangzhao , Lv Lei , Deng Yonghong , Wang Chaoyang 
Published: May 2017

Self‐healing hydrogels have been studied by many researchers via multiple cross‐linking approaches including physical and chemical interactions. It is an interesting project in multifunctional hydrogel exploration that a water soluble polymer matrix is cross‐linked by combining the ionic coordination and the multiple hydrogen bonds to fabricate self‐healing hydrogels with injectable property. This study introduces a general procedure of preparing the hydrogels (termed gelatin‐UPy‐Fe) cross‐linked by both ionic coordination of Fe3+ and carboxyl group from the gelatin and the quadruple hydrogen bonding interaction from the ureido‐pyrimidinone (UPy) dimers. The gelatin‐UPy‐Fe hydrogels possess an excellent self‐healing property. The effects of the ionic coordination of Fe3+ and quadruple hydrogen bonding of UPy on the formation and mechanical behavior of the prepared hydrogels are investigated. In vitro drug release of the gelatin‐UPy‐Fe hydrogels is also observed, giving an intriguing glimpse into possible biological applications.
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Development of Safe Drugs: The hERG Challenge
Authors: Kalyaanamoorthy Subha , Barakat Khaled H. 
Published: May 2017

AbstractDrug‐induced blockade of human ether‐a‐go‐go‐related gene (hERG) remains a major impediment in delivering safe drugs to the market. Several drugs have been withdrawn from the market due to their severe cardiotoxic side effects triggered by their off‐target interactions with hERG. Thus, identifying the potential hERG blockers at early stages of lead discovery is fast evolving as a standard in drug design and development. A number of in silico structure‐based models of hERG have been developed as a low‐cost solution to evaluate drugs for hERG liability, and it is now agreed that the hERG blockers bind at the large central cavity of the channel. Nevertheless, there is no clear convergence on the appropriate drug binding modes against the channel. The proposed binding modes differ in their orientations and interpretations on the role of key residues in the channel. Such ambiguities in the modes of binding remain to be a significant challenge in achieving efficient computational predictive models and in saving many important already Food and Drug Administration approved drugs. In this review, we discuss the spectrum of reported binding modes for hERG blockers, the various in silico models developed for predicting a drug's affinity to hERG, and the known successful optimization strategies to avoid off‐target interactions with hERG.
Efficient experimental designs for isotropic generalized diffusion tensor MRI (IGDTI)
Authors: Avram Alexandru V. , Sarlls Joelle E. , Hutchinson Elizabeth , Basser Peter J. 
Published: May 2017

PurposeWe propose a new generalized diffusion tensor imaging (GDTI) experimental design and analysis framework for efficiently measuring orientationally averaged diffusion‐weighted images (DWIs), which remove bulk signal modulations attributed to diffusion anisotropy and quantify isotropic higher‐order diffusion tensors (HOT). We illustrate how this framework accelerates the clinical measurement of rotation‐invariant tissue microstructural parameters derived from HOT, such as the HOT‐Trace and the mean t‐kurtosis.Theory and MethodsFor a large range of b‐values, we compare orientationally averaged DWIs measured with high angular resolution diffusion imaging to those obtained with the proposed isotropic GDTI (IGDTI) experimental design. We compare rotation‐invariant microstructural parameters measured with IGDTI to those derived from HOTs measured explicitly with GDTI.ResultsIn both fixed‐brain microimaging and in vivo clinical experiments, IGDTI accurately quantifies mean apparent diffusion coefficient (mADC)‐weighted DWIs over a wide range of b‐values and allows efficient computation of HOT‐derived scalar tissue parameters from a small number of DWIs.ConclusionsIGDTI provides direct and accurate estimates of orientationally averaged tissue water mobilities over a wide range of b‐values. This efficient method may enable new, sensitive, and quantitative assessments for clinical applications in which changes in mADC can be observe,d such as detecting and characterizing stroke, cancers, and neurodegenerative diseases. Magn Reson Med 79:180–194, 2018. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.
Quantification and tracking of genetically engineered dendritic cells for studying immunotherapy
Authors: Bar‐Shir Amnon , Alon Lina , Korrer Michael J. , Lim Hong Seo , Yadav Nirbhay N. , Kato Yoshinori , Pathak Arvind P. , Bulte Jeff W.M. , Gilad Assaf A. 
Published: May 2017

PurposeGenetically encoded reporters can assist in visualizing biological processes in live organisms and have been proposed for longitudinal and noninvasive tracking of therapeutic cells in deep tissue. Cells can be labeled in situ or ex vivo and followed in live subjects over time. Nevertheless, a major challenge for reporter systems is to identify the cell population that actually expresses an active reporter.MethodsWe have used a nucleoside analog, pyrrolo‐2′‐deoxycytidine, as an imaging probe for the putative reporter gene, Drosophila melanogaster 2′‐deoxynucleoside kinase. Bioengineered cells were imaged in vivo in animal models of brain tumor and immunotherapy using chemical exchange saturation transfer MRI. The number of transduced cells was quantified by flow cytometry based on the optical properties of the probe.ResultsWe performed a comparative analysis of six different cell lines and demonstrate utility in a mouse model of immunotherapy. The proposed technology can be used to quantify the number of labeled cells in a given region, and moreover is sensitive enough to detect less than 10,000 cells.ConclusionThis unique technology that enables efficient selection of labeled cells followed by in vivo monitoring with both optical and MRI. Magn Reson Med 79:1010–1019, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
Accelerated noncontrast‐enhanced 4‐dimensional intracranial MR angiography using golden‐angle stack‐of‐stars trajectory and compressed sensing with magnitude subtraction
Authors: Zhou Ziwu , Han Fei , Yu Songlin , Yu Dandan , Rapacchi Stanislas , Song Hee Kwon , Wang Danny J.J. , Hu Peng , Yan Lirong 
Published: May 2017

PurposeTo evaluate the feasibility and performance of compressed sensing (CS) with magnitude subtraction regularization in accelerating non–contrast‐enhanced dynamic intracranial MR angiography (NCE‐dMRA).MethodsA CS algorithm was introduced in NCE‐dMRA by exploiting the sparsity of the magnitude difference of the control and label images. The NCE‐dMRA data were acquired using golden‐angle stack‐of‐stars trajectory on six healthy volunteers and one patient with arteriovenous fistula. Images were reconstructed using (i) the proposed magnitude‐subtraction CS (MS‐CS); (ii) complex‐subtraction CS; (iii) independent CS; and (iv) view‐sharing with k‐space weighted image contrast (KWIC). The dMRA image quality was compared across the four reconstruction strategies. The proposed MS‐CS method was further compared with KWIC for temporal fidelity of depicting dynamic flow.ResultsThe proposed MS‐CS method was able to reconstruct NCE‐dMRA images with detailed vascular structures and clean background. It provided better subjective image quality than the other two CS strategies (P < 0.05). Compared with KWIC, MS‐CS showed similar image quality, but reduced temporal blurring in delineating the fine distal arteries.ConclusionsThe MS‐CS method is a promising CS technique for accelerating NCE‐dMRA acquisition without compromising image quality and temporal fidelity. Magn Reson Med 79:867–878, 2018. © 2017 International Society for Magnetic Resonance in Medicine.
The conventional tuning fork as a quantitative tool for vibration threshold
Authors: Alanazy Mohammed H. , Alfurayh Nuha A. , Almweisheer Shaza N. , Aljafen Bandar N. , Muayqil Taim 
Published: May 2017

ABSTRACTIntroduction: This study was undertaken to describe a method for quantifying vibration when using a conventional tuning fork (CTF) in comparison to a Rydel‐Seiffer tuning fork (RSTF) and to provide reference values. Methods: Vibration thresholds at index finger and big toe were obtained in 281 participants. Spearman's correlations were performed. Age, weight, and height were analyzed for their covariate effects on vibration threshold. Reference values at the fifth percentile were obtained by quantile regression. Results: The correlation coefficients between CTF and RSTF values at finger/toe were 0.59/0.64 (P = 0.001 for both). Among covariates, only age had a significant effect on vibration threshold. Reference values for CTF at finger/toe for the age groups 20–39 and 40–60 years were 7.4/4.9 and 5.8/4.6 s, respectively. Reference values for RSTF at finger/toe for the age groups 20–39 and 40–60 years were 6.9/5.5 and 6.2/4.7, respectively. Discussion: CTF provides quantitative values that are as good as those provided by RSTF. Age‐stratified reference data are provided. Muscle Nerve 57: 49–53, 2018
Clinical comparison of intravesical hyaluronic acid and chondroitin sulfate therapies in the treatment of bladder pain syndrome/interstitial cystitis
Authors: Gülpınar Ömer , Esen Barış , Kayış Aytaç , Gökçe Mehmet İlker , Süer Evren 
Published: May 2017

IntroductionIntravesical glucosaminoglycan (GAG) replacement therapies are commonly used in the treatment of bladder pain syndrome (BPS)/interstitial cystitis (IC). Different intravesical glucosaminoglycan products are currently available. In this prospective study, clinical efficacy of chondroitin sulfate and hyaluronic acid are compared in patients with BPS/IC.MethodsPatients were randomized to CS and HA groups. All patients were evaluated for visual analogue pain scale (VAS), interstitial cystitis symptom index (ICSI), interstitial cystitis problem index (ICPI), voiding diary for frequency/nocturia, and mean urine volume per void at the beginning of the therapy and after 6 months. All patients had a potassium sensitivity test (PST) initially. Wilcoxon and Mann‐Whitney U tests were used for statistical analysis.ResultsThere were 21 patients in both groups. Mean age of patients in CS and HA groups were 47.10 and 48.90, respectively(P > 0.05). Before treatment, Parson's test was positive in 64.3% of patients (27/42) with no difference between groups. VAS of pain, ICSI, ICPI, frequency at 24 h and nocturia results have improved significantly at both treatment arms. Intravesical CS was also found superior to intravesical HA in terms of 24 h frequency, nocturia and ICPI (P < 0.05). No severe adverse effects were reported.ConclusionsData comparing clinical efficiencies of different GAG therapies are very limited. In this study, intravesical CS was found superior to intravesical HA in terms of 24 h frequency, nocturia and ICPI in patients with BPS/IC in short term follow‐up. To provide a definitive conclusion on superiority of one GAG therapy to others, further evaluation with long term follow up is required.
Refining estimates of prescription durations by using observed covariates in pharmacoepidemiological databases: an application of the reverse waiting time distribution
Authors: Støvring Henrik , Pottegård Anton , Hallas Jesper 
Published: May 2017

AbstractPurposeThe study aimed to develop an automated method to estimate prescription durations in pharmacoepidemiological studies that may depend on patient and redemption characteristics.MethodsWe developed an estimation algorithm based on maximum likelihood estimation for the reverse waiting time distribution (WTD), which is the distribution of time from the last prescription of each patient within a time window to the end of the time window. The reverse WTD consists of two distinctly different components: one component for prevalent users and one for patients stopping treatment. We extended the model to allow parameters of the reverse WTD to depend on linear combinations of covariates to obtain estimates and confidence intervals for percentiles of the inter‐arrival density (time from one prescription to the subsequent). We applied the method to redemptions of warfarin, using the amount of drug filled, patient sex and patient age as covariates.ResultsThe estimated prescription durations increased with redeemed amount and age. Women generally had longer prescription durations, which increased more with age than men. For 70‐year‐old women redeeming 300+ pills, we predicted a 95th percentile of the inter‐arrival density of 225 (95%CI: 201, 249) days. For 50‐year‐old men redeeming 100 pills, the corresponding prediction was 97 (88, 106) days.ConclusionsThe algorithm allows estimation of prescription durations based on the reverse WTD, which can depend upon observed covariates. Statistical uncertainty intervals and tests allow statistical inference on the influence of observed patient and prescription characteristics. The method may replace ad hoc decision rules. Copyright © 2017 John Wiley & Sons, Ltd.
Cover Image, Volume 66, Issue 6
Authors: Purnama Aloisius R , Hennessy Matthew G , Vitale Alessandra , Cabral João T 
Published: May 2017

The cover image, by Aloisius R Purnama et al., is based on the Research Article Coarse‐grained models for frontal photopolymerization with evolving conversion profile, DOI: 10.1002/pi.5344.
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Refolding the unfoldable: A systematic approach for renaturation ofBacillus circulansxylanase
Authors: Kötzler Miriam P. , McIntosh Lawrence P. , Withers Stephen G. 
Published: May 2017

AbstractXylanases are important polysaccharide‐cleaving catalysts for the pulp and paper, animal feeds and biofuels industries. They have also proved to be valuable model systems for understanding enzymatic catalysis, with one of the best studied being the GH11 xylanase fromBacillus circulans(Bcx). However, proteins from this class are very recalcitrant to refoldingin vitro. This both limits their high level expression in heterologous hosts, and prevents experimental approaches, such as peptide ligation or chemical modifications, to probe and engineer their stability and function. To solve this problem, a systematic screening approach was employed to identify suitable buffer conditions for renaturing Bcxin vitro. The fractional factorial screen employed identified starting conditions for refolding, which were then refined and developed into a generic protocol for renaturing preparative amounts of active Bcx in a 50–60% yield from inclusion bodies. The method is robust and proved equally proficient at refolding circularly permuted versions that carry cysteine mutations. This general approach should be applicable to related GH11 xylanases, as well as proteins adopting a similar β‐jellyroll fold, that are otherwise recalcitrant to refoldingin vitro.
Carbohydrate recognition by the rhamnose‐binding lectin SUL‐I with a novel three‐domain structure isolated from the venom of globiferous pedicellariae of the flower sea urchin Toxopneustes pileolus
Authors: Hatakeyama Tomomitsu , Ichise Ayaka , Unno Hideaki , Goda Shuichiro , Oda Tatsuya , Tateno Hiroaki , Hirabayashi Jun , Sakai Hitomi , Nakagawa Hideyuki 
Published: May 2017

AbstractThe globiferous pedicellariae of the venomous sea urchin Toxopneustes pileolus contains several biologically active proteins. We have cloned the cDNA of one of the toxin components, SUL‐I, which is a rhamnose‐binding lectin (RBL) that acts as a mitogen through binding to carbohydrate chains on target cells. Recombinant SUL‐I (rSUL‐I) was produced in Escherichia coli cells, and its carbohydrate‐binding specificity was examined with the glycoconjugate microarray analysis, which suggested that potential target carbohydrate structures are galactose‐terminated N‐glycans. rSUL‐I exhibited mitogenic activity for murine splenocyte cells and toxicity against Vero cells. The three‐dimensional structure of the rSUL‐I/l‐rhamnose complex was determined by X‐ray crystallographic analysis at a 1.8 Å resolution. The overall structure of rSUL‐I is composed of three distinctive domains with a folding structure similar to those of CSL3, a RBL from chum salmon (Oncorhynchus keta) eggs. The bound l‐rhamnose molecules are mainly recognized by rSUL‐I through hydrogen bonds between its 2‐, 3‐, and 4‐hydroxy groups and Asp, Asn, and Glu residues in the binding sites, while Tyr and Ser residues participate in the recognition mechanism. It was also inferred that SUL‐I may form a dimer in solution based on the molecular size estimated via dynamic light scattering as well as possible contact regions in its crystal structure.