bluuebunny/crossref_metadata_2025 huggingface dataset:
Reactions of Diazomethanes with 5‐Benzylidene‐3‐phenylrhodanine – A Computational Study
Authors: Khlebnikov Alexander F. , Seyfried Martin S. , Heimgartner Heinz
Published: February 2016

It has been shown previously that the reaction of diazomethane with 5‐benzylidene‐3‐phenylrhodanine (1) in THF at −20° occurs at the exocyclic CC bondviacyclopropanation to give3aand methylation to yield4, respectively, whereas the corresponding reaction with phenyldiazomethane in toluene at 0° leads to the cyclopropane derivative3bexclusively. Surprisingly, under similar conditions, no reaction was observed between1and diphenyldiazomethane, but the 2‐diphenylmethylidene derivative5was formed in boiling toluene. In the present study, these results have been rationalized by calculations at the DFT B3LYP/6‐31G(d) level using PCM solvent model. In the case of diazomethane, the formation of3aoccursviainitialMichaeladdition, whereas4is formedvia[3+2] cycloaddition followed by N2elimination and H‐migration. The preferred pathway of the reaction of1with phenyldiazomethane is a [3+2] cycloaddition, subsequent N2elimination and ring closure of an intermediate zwitterion to give3b. Finally, the calculations show that the energetically most favorable reaction of1with diphenyldiazomethane is the initial formation of diphenylcarbene, which adds to the S‐atom to give a thiocarbonyl ylide, followed by 1,3‐dipolar electrocyclization and S‐elimination.
Novel Protein Arginine Methyltransferase 8 Isoform Is Essential for Cell Proliferation
Authors: Hernandez Sarah , Dominko Tanja
Published: February 2016

Identification of molecular mechanisms that regulate cellular replicative lifespan is needed to better understand the transition between a normal and a neoplastic cell phenotype. We have previously reported that low oxygen‐mediated activity of FGF2 leads to an increase in cellular lifespan and acquisition of regeneration competence in human dermal fibroblasts (iRC cells). Though cells display a more plastic developmental phenotype, they remain non‐tumorigenic when injected into SCID mice (Page et al. [2009] Cloning Stem Cells 11:417–426; Page et al. [2011] Eng Part A 17:2629–2640) allowing for investigation of mechanisms that regulate increased cellular lifespan in a non‐tumorigenic system. Analysis of chromatin modification enzymes by qRT‐PCR revealed a 13.3‐fold upregulation of the arginine methyltransferase PRMT8 in iRC cells. Increased protein expression was confirmed in both iRC and human embryonic stem cells—the first demonstration of endogenous human PRMT8 expression outside the brain. Furthermore, iRC cells express a novel PRMT8 mRNA variant. Using siRNA‐mediated knockdown we demonstrated that this novel variant was required for proliferation of human dermal fibroblasts (hDFs) and grade IV glioblastomas. PRMT8 upregulation in a non‐tumorigenic system may offer a potential diagnostic biomarker and a therapeutic target for cells in pre‐cancerous and cancerous states. J. Cell. Biochem. 117: 2056–2066, 2016. © 2016 Wiley Periodicals, Inc.
Effects of the Histamine 1 Receptor Antagonist Cetirizine on the Osteoporotic Phenotype in H+/K+ATPase Beta Subunit KO Mice
Authors: Aasarød Kristin M. , Stunes Astrid K. , Mosti Mats P. , Ramezanzadehkoldeh Masoud , Viggaklev Bjørn I. , Reseland Janne E. , Skallerud Bjørn H. , Fossmark Reidar , Syversen Unni
Published: February 2016

Epidemiological studies suggest increased fracture risk in patients using proton pump inhibitors (PPIs). We have previously shown that the H+/K+ATPase beta subunit knockout (KO) mouse, which is a model of PPI‐use, have lower bone mineral density (BMD) and impaired bone quality compared to wild type (WT) mice. Like PPI users, these KO mice display elevated gastric pH and hypergastrinemia, which in turn stimulates gastric histamine release. Previous studies have suggested a negative effect of histamine on bone, thus, we wanted to study whether a histamine 1 receptor (H1R) antagonist could improve bone quality in KO mice. Female KO and WT mice aged 8 weeks received either an H1R antagonist (cetirizine) or polyethylene glycol (PEG) for 6 months. At the end of the study, KO mice displayed elevated plasma histamine levels compared to WT. As demonstrated previously, the KO mice also exhibited lower whole body BMD, reduced mechanical bone strength, and impaired bone quality assessed by μCT. No significant differences, however, were found between the KO groups receiving cetirizine or PEG for any of the measured bone parameters. In vitro gene expression analyses of histamine receptors revealed the presence of H1R and H2R both in osteoblasts and osteoclasts, and H3R in late stage osteoblasts. In conclusion, administration of the H1R antagonist cetirizine in a concentration of 3 mg/kg did not rescue the osteoporotic phenotype in H+/K+ATPase beta subunit KO mice. It can, however, not be ruled out that histamine may influence bone via other receptors. J. Cell. Biochem. 117: 2089–2096, 2016. © 2016 Wiley Periodicals, Inc.
Bounds on the Dimensions of 2‐Spontaneous Emission Error Designs
Authors: Zhou Junling , Chang Yanxun
Published: February 2016

Quantum jump codes are quantum error‐correcting codes which correct errors caused by quantum jumps. A t‐spontaneous emission error design (t‐SEED) was introduced by Beth et al. in 2003 [T. Beth, C. Charnes, M. Grassl, G. Alber, A. Delgado, and M. Mussinger, A new class of designs which protect against quantum jumps, Des Codes Cryptogr 29 (2003), 51–70.] to construct quantum jump codes. The number of designs (dimension) in a t‐SEED corresponds to the number of orthogonal basis states in a quantum jump code. A nondegenerate t‐SEED is optimal if it has the largest possible dimension. In this paper, we investigate the bounds on the dimensions of 2‐SEEDs systematically. The exact dimensions of optimal 2‐ SEEDs are almost determined, with five possible exceptions in doubt. General upper bounds on dimensions of 2‐ SEEDs are demonstrated, the corresponding leave graphs are described, and several exceptional cases are studied in details. Meanwhile, we employ 2‐homogenous groups to obtain new lower bounds on the dimensions of 2‐ SEEDs for prime power orders v and general block sizes k.
A review of biomass energy – shortcomings and concerns
Authors: Rosillo‐Calle Frank
Published: February 2016

Biomass has been, historically, the main source of global energy, primarily for cooking, heating, and small cottage industries. It is witnessing a strong revival and is currently used in a multitude of applications. It provides between 10 and 14% of world energy, with the potential to provide 30–40 + % and is an integral component of all energy scenarios. Biomass energy is providing multiple energy, environmental, and socio‐economic benefits, both modern and traditional, ranging from electricity, heat, to transportation fuels.

This review provides a critical assessment of biomass energy literature. It is not an analysis of biomass energy production and conversion methods. The main themes covered are: (i) biomass energy potential and its uses; (ii) liquid biofuels for transportation; (iii) land use changes implications; (iv) the food versus fuel debate; (v) environmental and sustainability, subsidies and energy balance issues; and (vi) international biomass energy trade. An additional key concern of this review has been to identify the main shortcomings and concerns affecting biomass energy of themes stated above, e.g. problems posed by poor scientific data, land use change, food versus biofuel debate; environmental and sustainability implications, or potential impacts of international biomass energy trade. Given the broad nature of biomass energy, and the need to embraces all major issues, this review paper is in many ways an overview. © 2016 Society of Chemical Industry
Re‐evaluation of batoid pectoral morphology reveals novel patterns of diversity among major lineages
Authors: Martinez Christopher M. , Rohlf F. James , Frisk Michael G.
Published: February 2016

Batoids (Chondrichthyes: Batoidea) are a diverse group of cartilaginous fishes which comprise a monophyletic sister lineage to all neoselachians or modern sharks. All species in this group possess anteroposteriorly expanded‐pectoral fins, giving them a unique disc‐like body form. Reliance on pectoral fins for propulsion ranges from minimal (sawfish) to almost complete dependence (skates and rays). A recent study on the diversity of planform pectoral fin shape in batoids compared overall patterns of morphological variation within the group. However, inconsistent pectoral homology prevented the study from accurately representing relationships within and among major batoid taxa. With previous work in mind, we undertook an independent investigation of pectoral form in batoids and evaluated the implications of shape diversity on locomotion and lifestyle, particularly in the skates (Rajoidei) and rays (Myliobatoidei). We used geometric morphometrics with sliding semilandmarks to analyze pectoral fin outlines and also calculate fin aspect ratios (AR), a functional trait linked to locomotion. In agreement with previous work, our results indicated that much of the evolution of batoid pectoral shape has occurred along a morphological axis that is closely related to AR. For species where kinematic data were available, both shape and AR were associated with swimming mode. This work further revealed novel patterns of shape variation among batoids, including strong bimodality of shape in rays, an intermediate location of skate species in the morphospace between benthic/demersal and pelagic rays, and approximately parallel shape trajectories in the benthic/demersal rays and skates. Finally, manipulation of landmarks verified the need for a consistent and accurate definition of homology for the outcome and efficacy of analyses of pectoral form and function in batoids. J. Morphol. 277:482–493, 2016. © 2016 Wiley Periodicals, Inc.
Ontogeny of head and caudal fin shape of an apex marine predator: The tiger shark (Galeocerdo cuvier)
Authors: Fu Amy L. , Hammerschlag Neil , Lauder George V. , Wilga Cheryl D. , Kuo Chi‐Yun , Irschick Duncan J.
Published: February 2016

How morphology changes with size can have profound effects on the life history and ecology of an animal. For apex predators that can impact higher level ecosystem processes, such changes may have consequences for other species. Tiger sharks (Galeocerdo cuvier) are an apex predator in tropical seas, and, as adults, are highly migratory. However, little is known about ontogenetic changes in their body form, especially in relation to two aspects of shape that influence locomotion (caudal fin) and feeding (head shape). We captured digital images of the heads and caudal fins of live tiger sharks from Southern Florida and the Bahamas ranging in body size (hence age), and quantified shape of each using elliptical Fourier analysis. This revealed changes in the shape of the head and caudal fin of tiger sharks across ontogeny. Smaller juvenile tiger sharks show an asymmetrical tail with the dorsal (upper) lobe being substantially larger than the ventral (lower) lobe, and transition to more symmetrical tail in larger adults, although the upper lobe remains relatively larger in adults. The heads of juvenile tiger sharks are more conical, which transition to relatively broader heads over ontogeny. We interpret these changes as a result of two ecological transitions. First, adult tiger sharks can undertake extensive migrations and a more symmetrical tail could be more efficient for swimming longer distances, although we did not test this possibility. Second, adult tiger sharks expand their diet to consume larger and more diverse prey with age (turtles, mammals, and elasmobranchs), which requires substantially greater bite area and force to process. In contrast, juvenile tiger sharks consume smaller prey, such as fishes, crustaceans, and invertebrates. Our data reveal significant morphological shifts in an apex predator, which could have effects for other species that tiger sharks consume and interact with. J. Morphol. 277:556–564, 2016. © 2016 Wiley Periodicals, Inc.
Assessment of the precision and reproducibility of ventricular volume, function, and mass measurements with ferumoxytol‐enhanced 4D flow MRI
Authors: Hanneman Kate , Kino Aya , Cheng Joseph Y. , Alley Marcus T. , Vasanawala Shreyas S.
Published: February 2016

Purpose

To compare the precision and interobserver agreement of ventricular volume, function, and mass quantification by 3D time‐resolved (4D) flow MRI relative to cine steady‐state free precession (SSFP).

Materials and Methods

With Institutional Research Board approval, informed consent, and HIPAA compliance, 22 consecutive patients with congenital heart disease (CHD) (10 males, 6.4 ± 4.8 years) referred for 3T ferumoxytol‐enhanced cardiac MRI were prospectively recruited. Complete ventricular coverage with standard 2D short‐axis cine SSFP and whole chest coverage with axial 4D flow were obtained. Two blinded radiologists independently segmented images for left ventricular (LV) and right ventricular (RV) myocardium at end systole (ES) and end diastole (ED). Statistical analysis included linear regression, analysis of variance (ANOVA), Bland–Altman (BA) analysis, and intraclass correlation (ICC).

Results

Significant positive correlations were found between 4D flow and SSFP for ventricular volumes (r = 0.808–0.972, P < 0.001), ejection fraction (EF) (r = 0.900–928, P < 0.001), and mass (r = 0.884–0.934, P < 0.001). BA relative limits of agreement for both ventricles were between –52% to 34% for volumes, –29% to 27% for EF, and –41% to 48% for mass, with wider limits of agreement for the RV compared to the LV. There was no significant difference between techniques with respect to mean square difference of ED‐ES mass for either LV (F = 2.05, P = 0.159) or RV (F = 0.625, P = 0.434). Interobserver agreement was moderate to good with both 4D flow (ICC 0.523–0.993) and SSFP (ICC 0.619–0.982), with overlapping confidence intervals.

Conclusion

Quantification of ventricular volume, function, and mass can be accomplished with 4D flow MRI with precision and interobserver agreement comparable to that of cine SSFP. J. Magn. Reson. Imaging 2016;44:383–392.
Variations in medial‐lateral hamstring force and force ratio influence tibiofemoral kinematics
Authors: Shalhoub Sami , Fitzwater Fallon G. , Cyr Adam J. , Maletsky Lorin P.
Published: February 2016

A change in hamstring strength and activation is typically seen after injuries or invasive surgeries such as anterior cruciate reconstruction or total knee replacement. While many studies have investigated the influence of isometric increases in hamstring load on knee joint kinematics, few have quantified the change in kinematics due to a variation in medial to lateral hamstring force ratio. This study examined the changes in knee joint kinematics on eight cadaveric knees during an open‐chain deep knee bend for six different loading configurations: five loaded hamstring configurations that varied the ratio of a total load of 175 N between the semimembranosus and biceps femoris and one with no loads on the hamstring. The anterior–posterior translation of the medial and lateral femoral condyles’ lowest points along proximal‐distal axis of the tibia, the axial rotation of the tibia, and the quadriceps load were measured at each flexion angle. Unloading the hamstring shifted the medial and lateral lowest points posteriorly and increased tibial internal rotation. The influence of unloading hamstrings on quadriceps load was small in early flexion and increased with knee flexion. The loading configuration with the highest lateral hamstrings force resulted in the most posterior translation of the medial lowest point, most anterior translation of the lateral lowest point, and the highest tibial external rotation of the five loading configurations. As the medial hamstring force ratio increased, the medial lowest point shifted anteriorly, the lateral lowest point shifted posteriorly, and the tibia rotated more internally. The results of this study, demonstrate that variation in medial‐lateral hamstrings force and force ratio influence tibiofemoral transverse kinematics and quadriceps loads required to extend the knee. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1707–1715, 2016.
Hyaluronic acid versus saline intra‐articular injections for amelioration of chronic knee osteoarthritis: A canine model
Authors: Pashuck Troy D. , Kuroki Keiichi , Cook Cristi R. , Stoker Aaron M. , Cook James L.
Published: February 2016

The objective of this study was to assess the safety and efficacy of intra‐articular injections of hyaluronic acid (HA) versus saline for symptomatic treatment of osteoarthritis (OA). Twenty‐five adult purpose‐bred dogs underwent meniscal release of one knee. Clinical, arthroscopic, and radiographic signs of OA were confirmed in all dogs prior to treatment. Dogs were randomized into five groups: HA‐1 (n = 5), HA‐3 (n = 5), HA‐5 (n = 5), Saline‐1 (n = 5), and Saline‐3 (n = 5). Each dog received intra‐articular injections of the respective substance into the affected knee at the pre‐determined time points. Dogs were assessed for heat, swelling, and erythema after each injection and for lameness, pain, effusion, range of motion, kinetics, radiographic OA scoring, and arthroscopic scoring prior to treatment and for 6 months after injection. Dogs were then humanely euthanatized and the knees assessed grossly and histologically. Only mild heat, swelling, and/or erythema were noted in some dogs following injection and resolved within 1 week. Dogs treated with HA‐1, HA‐3, and HA‐5 were significantly (p < 0.05) better than dogs treated with Saline‐1 and Saline‐3 at the 4, 8, and 12 week time points based on at least one outcome measure. OA severity was not significantly different among groups at any time point, but increased in severity over time in all groups. Gross and histologic OA scores were not significantly different among groups. These data suggest the three HA injection protocols were safe, superior to saline for short‐term amelioration of symptoms associated with chronic OA, and can be translated to human OA treatment. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1772–1779, 2016.
On The Role of Wetting, Structure Width, and Flow Characteristics in Polymer Replication on Micro‐ and Nanoscale
Authors: Rytka Christian , Opara Nadia , Andersen Nis Korsgaard , Kristiansen Per Magnus , Neyer Andreas
Published: February 2016

The replication of functional polymeric micro‐ and nanostructures requires a deep understanding of material and process interrelations. In this investigation the dewetting potential of a polymer is proposed as a simple rationale for estimation of the replicability of functional micro‐ and nanostructures by injection molding. The dewetting potential of a polymer is determined by integrating the spreading coefficient over the range from melt temperature to no‐flow temperature. From all polymers tested, the lowest dewetting potential is calculated for PP and the highest for polymethylmethacrylate. The dewetting potential correlates well with the replicated height of four different structures covering both the micro‐ and the nanorange on two different surfaces (brass and fluorocarbon modified nickel) and polymers with different spreading coefficients. It is clearly shown that a lower dewetting potential of a polymer leads to a better replication accuracy. Additionally a parabolic relationship is demonstrated between filled height and structure width.

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Standardized Assessment of Hereditary Ataxia Patients in Clinical Studies
Authors: Paap Brigitte K. , Roeske Sandra , Durr Alexandra , Schöls Ludger , Ashizawa Tetsuo , Boesch Sylvia , Bunn Lisa M. , Delatycki Martin B. , Giunti Paola , Lehéricy Stéphane , Mariotti Caterina , Melegh Jörg , Pandolfo Massimo , Tallaksen Chantal M.E. , Timmann Dagmar , Tsuji Shoji , Schulz Jörg Bela , van de Warrenburg Bart P. , Klockgether Thomas
Published: February 2016

Background

Hereditary ataxias are a heterogeneous group of degenerative diseases of the cerebellum, brainstem, and spinal cord. They may present with isolated ataxia or with additional symptoms going beyond cerebellar deficits. There are an increasing number of clinical studies with the goal to define the natural history of these disorders, develop biomarkers, and investigate therapeutic interventions. Especially, early and preclinical disease stages are currently of particular interest.

Methods and Results

Evidence‐based, we review standards for sampling and storage of biomaterials, clinical and neuropsychological assessment, as well as neurophysiology and neuroimaging and recommendations for standardized assessment of ataxia patients in multicenter studies.

Conclusions

DNA, RNA, serum, and, if possible, cerebrospinal fluid samples should be processed following established standards. Clinical assessment in ataxia studies must include use of a validated clinical ataxia scale. There are several validated clinical ataxia scales available. There are no instruments that were specifically designed for assessing neuropsychological and psychiatric symptoms in ataxia disorders. We provide a list of tests that may prove valuable. Quantitative performance tests have the potential to supplement clinical scales. They provide additional objective and quantitative information. Posturography and quantitative movement analysis—despite valid approaches—require standardization before implemented in multicenter studies. Standardization of neurophysiological tools, as required for multicenter interventional trials, is still lacking. Future multicenter neuroimaging studies in ataxias should implement quality assurance measures as defined by the ADNI or other consortia. MRI protocols should allow morphometric analyses.
Epidemiology of myasthenia gravis in Northern Portugal: Frequency estimates and clinical epidemiological distribution of cases
Authors: Santos Ernestina , Coutinho Ester , Moreira Isabel , Silva Ana Martins , Lopes Dina , Costa Henrique , Silveira Fernando , Nadais Goreti , Morais Hugo , Martins João , Branco Maria Ceu , Veiga Andreia , Silva Rosa Santos , Ferreira Augusto , Sousa Filipa , Freijo Marta , Matos Ilda , André Rui , Negrão Luís , Fraga Carla , Santos Manuela , Sampaio Mafalda , Lopes Carlos , Leite Maria Isabel , Gonçalves Guilherme
Published: February 2016

Introduction: In this study we estimated the prevalence, incidence, and mortality of myasthenia gravis (MG) in northern Portugal and characterized the clinical features of the patients identified. Methods: We used 2 data sources: clinical records from the hospitals and pyridostigmine prescription registers. Results: On December 31, 2013, we estimated a point prevalence of 111.7 patients per million population. The highest prevalence was observed in the group >65 years of age, especially in men (288.1 per million). During 2013, we estimated an incidence rate of 6.3 per million per year. Among women, the incidence rate was highest in the 15–49‐year age group; in men, incidence increased with age up to 22.1 per million in those >65 years old. The MG‐related mortality rate was 0.5 per million. Conclusions: These figures are in keeping with similar studies and emphasize the importance of diagnosis and management of MG in elderly populations. Muscle Nerve 54: 413–421, 2016
Perception of pain during electromyography in children: A prospective study
Authors: Alshaikh Nahla M. , Martinez Jeimmy Pinzon , Pitt Matthew C.
Published: February 2016

Introduction

Electrodiagnostic examination is perceived as a painful examination. An accurate assessment of its discomfort would be valuable to children, their parents, and clinicians.

Methods

We performed a prospective study of pediatric patients seen over 3 months at 1 center. Pain was scored for both nerve conduction studies and needle electromyography (EMG) on validated scales, depending on the child's age and in comparison with venipuncture.

Results

In 100 cases the pain recorded fell within the moderate range on the scoring systems used. Sixty‐six percent of patients described the pain to be equivalent or less than that with venipuncture. EMG of > 1 muscle or a proximal muscle produced more pain in patients <4 years of age.

Conclusions

When discussing the test with patients, the physician should reassure the patient and parents regarding the degree of pain that may be encountered, which is not materially different from venipuncture. Muscle Nerve 54: 422–426, 2016
Bone marrow segmentation based on a combined consideration of transverse relaxation processes and Dixon oscillations
Authors: Balasubramanian Mukund , Jarrett Delma Y. , Mulkern Robert V.
Published: February 2016

The aim of this study was to demonstrate that gradient‐echo sampling of single spin echoes can be used to isolate the signal from trabecular bone marrow, with high‐quality segmentation and surface reconstructions resulting from the application of simple post‐processing strategies.

Theoretical expressions of the time‐domain single‐spin‐echo signal were used to simulate signals from bone marrow, non‐bone fatty deposits and muscle. These simulations were compared with and used to interpret signals obtained by the application of the gradient‐echo sampling of a spin‐echo sequence to image the knee and surrounding tissues at 1.5 T.

Trabecular bone marrow has a much higher reversible transverse relaxation rate than surrounding non‐bone fatty deposits and other musculoskeletal tissues. This observation, combined with a choice of gradient‐echo spacing that accentuates Dixon‐type oscillations from chemical‐shift interference effects, enabled the isolation of bone marrow signal from surrounding tissues through the use of simple image subtraction and thresholding. Three‐dimensional renderings of the marrow surface were then readily generated with this approach – renderings that may prove useful for bone morphology assessment, e.g. for the measurement of femoral anteversion.

In conclusion, understanding the behavior of signals from bone marrow and surrounding tissue as a function of time through a spin echo facilitates the segmentation and reconstruction of bone marrow surfaces using straightforward post‐processing strategies that are typically available on modern radiology workstations. Copyright © 2016 John Wiley & Sons, Ltd.
Neurological PRESentations in Sickle Cell Patients Are Not Always Stroke: A Review of Posterior Reversible Encephalopathy Syndrome in Sickle Cell Disease
Authors: Solh Ziad , Taccone Michael S. , Marin Samantha , Athale Uma , Breakey Vicky R.
Published: February 2016

Acute neurological changes in sickle cell disease (SCD) patients often raise the suspicion for stroke. Posterior reversible encephalopathy syndrome (PRES) can mimic stroke in its clinical presentation. We aimed to (i) review the PRES literature in SCD patients including clinical presentation, risk factors, pathophysiology, and management and (ii) elucidate the distinction between PRES and stroke in SCD. The exact pathophysiology of PRES in SCD remains elusive but is likely multifactorial and related to sickling, ischemia, and chronic anemia predisposing to vasogenic edema. PRES and stroke in SCD are distinguishable conditions. Our review may help elucidate a clinical approach to this distinction.
Poly[(3‐hydroxybutyrate)‐co‐(3‐hydroxyvalerate)] active bilayer films obtained by compression moulding and applying essential oils at the interface
Authors: Requena Raquel , Jiménez Alberto , Vargas María , Chiralt Amparo
Published: February 2016

Four active components, oregano essential oil (OR) and its respective main compound carvacrol (CA) and clove essential oil (CLO) and its respective main compound eugenol (EU), were used separately to obtain, using compression moulding, poly[(3‐hydroxybutyrate)‐co‐(3‐hydroxyvalerate)] (PHBV) bilayer films with antimicrobial activity. The active compounds were sprayed (15% w/w, polymer to active compound ratio) at the interface between two layers of PHBV, which were joined using thermo‐compression. Tensile, barrier and optical properties, as well as thermal behaviour, of the films were characterized after one week at 25 °C and 53% relative humidity. Likewise, the antimicrobial activity of the films was evaluated against Escherichia coli and Listeria innocua. Although the tensile properties of the films were not improved with respect to pure PHBV films by the addition of the active compounds, more transparent materials with better water vapour barrier capacity were obtained. Thermogravimetric analyses showed that CA and EU slightly decreased the polymer thermal stability, while OR and CLO led to more thermally resistant material. Miscibility of actives with the polymer was assessed through the promoted decrease in melting temperature and degree of crystallinity. PHBV films allowed the release of the active compounds in adequate amounts and at adequate rates into culture media to control the microbial growth of the two tested bacteria. The films were significantly more effective against E. coli than against L. innocua. Both bacteria were more sensitive to OR and to its main compound, CA, due to the greater antimicrobial effectiveness of these components. © 2016 Society of Chemical Industry
The respective roles of polar/nonpolar binary patterns and amino acid composition in protein regular secondary structures explored exhaustively using hydrophobic cluster analysis
Authors: Rebehmed Joseph , Quintus Flavien , Mornon Jean‐Paul , Callebaut Isabelle
Published: February 2016

Several studies have highlighted the leading role of the sequence periodicity of polar and nonpolar amino acids (binary patterns) in the formation of regular secondary structures (RSS). However, these were based on the analysis of only a few simple cases, with no direct mean to correlate binary patterns with the limits of RSS. Here, HCA‐derived hydrophobic clusters (HC) which are conditioned binary patterns whose positions fit well those of RSS, were considered. All the HC types, defined by unique binary patterns, which were commonly observed in three‐dimensional (3D) structures of globular domains, were analyzed. The 180 HC types with preferences for either α‐helices or β‐strands distinctly contain basic binary units typical of these RSS. Therefore a general trend supporting the “binary pattern preference” assumption was observed. HC for which observed RSS are in disagreement with their expected behavior (discordant HC) were also examined. They were separated in HC types with moderate preferences for RSS, having “weak” binary patterns and versatile RSS and HC types with high preferences for RSS, having “strong” binary patterns and then displaying nonpolar amino acids at the protein surface. It was shown that in both cases, discordant HC could be distinguished from concordant ones by well‐differentiated amino acid compositions. The obtained results could, thus, help to complement the currently available methods for the accurate prediction of secondary structures in proteins from the only information of a single amino acid sequence. This can be especially useful for characterizing orphan sequences and for assisting protein engineering and design. Proteins 2016; 84:624–638. © 2016 Wiley Periodicals, Inc.
The 3‐method for thermal conductivity measurements in a bottom heater geometry
Authors: Feuchter Manuel , Jooss Christian , Kamlah Marc
Published: February 2016

In this article, we investigate a bottom heater geometry configuration for the 3‐method, to determine the thermal conductivity of bulk‐like materials and thin covering layer materials. By finite element simulations, the temperature oscillations due to AC Joule heating are calculated in the time domain. Based on these calculations an understanding is developed for the dependence of the temperature amplitude on thermal conductivity and the chosen geometries. Since no closed form solution exists for these configurations, we developed a new evaluation methodology in order to identify the thermal conductivity of the investigated material. We discuss the determination of the cross‐plane thermal conductivity of materials in bulk and thin film geometries and verify the obtained result by an experiment, where a SrTiO thin film is deposited on top of a Pt heater.
Elucidation and identification of amino acid containing membrane lipids using liquid chromatography/high‐resolution mass spectrometry
Authors: Moore Eli K. , Hopmans Ellen C. , Rijpstra W. Irene C. , Villanueva Laura , Sinninghe Damsté Jaap S.
Published: February 2016

Rationale

Intact polar lipids (IPLs) are the building blocks of cell membranes, and amino acid containing IPLs have been observed to be involved in response to changing environmental conditions in various species of bacteria. High‐performance liquid chromatography/mass spectrometry (HPLC/MS) has become the primary method for analysis of IPLs. Many glycerol‐free amino acid containing membrane lipids (AA‐IPLs), which are structurally different than abundant aminophospholipids, have not been characterized using HPLC/MS. This results in many lipids remaining unrecognized in IPL analysis of microbial cultures and environmental samples, hampering the study of their occurrence and functionality.

Methods

We analyzed the amino acid containing IPLs of a number of bacteria (i.e. Gluconobacter cerinus, Cyclobacterium marinus, Rhodobacter sphaeroides, and Pedobacter heparinus) in order to decipher fragmentation pathways, and explore potential novel lipid structures using HPLC/electrospray ionization ion trap MS (HPLC/ESI‐IT‐MS) and HPLC/high‐resolution MS (HPLC/HRMS).

Results

We report differentiation between glutamine and lysine lipids with the same nominal masses, novel MS fragmentation pathways of cytolipin, the lipopeptides cerilipin and flavolipin, head group hydroxylated ornithine lipids, and the novel identification of cerilipin with a hydroxylated fatty acid.

Conclusions

Non‐glycerol AA lipids can be readily recognized as their fragmentation follows a clear pattern with initial dehydration or other loss from the head group, followed by fatty acid losses resulting in a diagnostic fragment ion. Higher level MSn and HRMS are valuable tools in characterizing AA lipid head group structural components. Copyright © 2016 John Wiley & Sons, Ltd.
Context and Implications Document for: Models of learning space: integrating research on space, place and learning in higher education
Authors: Ellis R. A. , Goodyear P.
Published: February 2016

This guide accompanies the following article: R. A. Ellis and P. Goodyear (2016) Models of learning space: integrating research on space, place and learning in higher education. Review of Education, DOI:10.1002/rev3.3056
Predicting health outcomes from high‐dimensional longitudinal health histories using relational random forests
Authors: Shahn Zach , Ryan Patrick , Madigan David
Published: February 2016

With the rise of Electronic Health Records (EHRs), there is increasing interest in algorithms that predict health outcomes from health histories. However, it is challenging to translate all the potentially relevant information contained in a health history into a format that would be manageable for traditional machine learning algorithms. Specifically, it would be desirable to incorporate relative temporal relationships among multiple health events, a task made difficult by the vastness of the space of such predictors. To this end, we modify and repurpose a predictive modeling method (referred to in the remainder as Random Relational Forest, or RRF) originally developed in the context of speech recognition. RRF generates informative labeled graphs representing temporal relations among health events at the nodes of randomized decision trees. We illustrate the utility of RRF by predicting strokes in patients with prior diagnoses of Atrial Fibrillation (afib) and demonstrate potentially clinically meaningful improvements over more traditional predictive models.
Discovering an active subspace in a single‐diode solar cell model
Authors: Constantine Paul G. , Zaharatos Brian , Campanelli Mark
Published: February 2016

Predictions from science and engineering models depend on the values of the model's input parameters. As the number of parameters increases, algorithmic parameter studies such as optimization and uncertainty quantification require many more model evaluations. One way to combat this curse of dimensionality is to seek an alternative parameterization with fewer variables that produces comparable predictions. The active subspace is a low‐dimensional linear subspace defined by important directions in the model's input space; input perturbations along these directions change the model's prediction more, on average, than perturbations orthogonal to the important directions. We describe a method for checking if a model admits an exploitable active subspace and apply this method to a single‐diode solar cell model with five input parameters. We find that the maximum power of the solar cell has a dominant one‐dimensional active subspace, which enables us to perform thorough parameter studies in one dimension instead of five.
Modeling supernovae light curves: An application of hierarchical smoothing splines
Authors: Reese C. Shane , Spencer Brittany S. , Ball Erika L.
Published: February 2016

With large data collection projects such as the Dark Energy Survey underway, data from distant supernovae (SNe) are becoming increasingly available. As the quantity of information increases, the ability to quickly and accurately classify SNe has become essential. An area of great interest is the development of a strictly photometric classification mechanism. The first step in the advancement of modern photometric classification is the estimation of individual Supernova (SN) light curves. We propose the use of hierarchical Gaussian processes to model light curves. Individual SN light curves are assigned a Gaussian process prior centered at a type‐specific mean curve which is also assigned a Gaussian process prior. Properties inherent in this Bayesian non‐parametric form of modeling yield flexible yet smooth curves estimates with a unique quantification of the error surrounding these curve estimates. Specifying the hierarchical structure relates individual SN light curves in such a way that borrowing strength across curves is possible. This allows for the estimation of SN light curves in entirety even when data are sparse. Additionally, it also yields a meaningful representation of SN class differences in the form of mean curves. The differences inherent in these mean curves may eventually allow for classification of SNe.
Influence of Natural and Accelerated Carbonation of Steel Slags on Their Leaching Behavior
Authors: Spanka Marina , Mansfeldt Tim , Bialucha Ruth
Published: February 2016

The influence of natural and accelerated carbonation on the leaching behavior of a basic oxygen furnace slag (BOS), electric arc furnace slag from carbon steel production (EAF C), and electric arc furnace slag from high‐alloy/stainless steel production (EAF S) has been investigated in this study. The carbonation reaction is examined using two experimental series: (i) outdoor‐exposure tests; and (ii) accelerated carbonation treatments in the laboratory. The achieved leaching results for the exposed steel slags show a distinct increase in Si and V concentrations and a decrease of Ca, with lower pH, due to carbonation. The other elements (Al, Cr, F, and Mo) react differently to carbonation depending on the mineral binding. However, the achieved results show that the German LAGA emplacement category can be improved from Z 2, for restricted applications with defined safeguarding measures, to Z 1 restricted open applications, due to carbonation. With regard to the storage of carbon dioxide (CO2) in slags and CO2 reduction of the atmosphere, the EAF S appears to be best suited for carbonation, because this slag reveals the highest CO2 uptake. Moreover, for this slag type significant decreases of the leached amount of Al, Ca, Cr, and Mo could be achieved.
Application of a Modified Stress−Strain Approach for the Fatigue‐Life Prediction of a Ferritic, an Austenitic and a Ferritic–Austenitic Duplex Steel under Isothermal and Thermo‐Mechanical Fatigue
Authors: Kulawinski Dirk , Kolmorgen Roman , Biermann Horst
Published: February 2016

The isothermal and thermo‐mechanical fatigue behavior of the ferritic–austenitic duplex stainless steel X2CrNiMoN22‐5‐3 is investigated in the temperature range of 100–600 °C. Furthermore, isothermal and thermo‐mechanical fatigue tests on single‐phase ferritic and austenitic reference steels are carried out within the same temperature range. A recently developed fatigue‐lifetime description is applied and modified for all tests as well as on the different steels individually, providing appropriate fatigue‐life predictions.
Inhibition of MDA‐MB‐231 breast cancer cell proliferation and tumor growth by apigenin through induction of G2/M arrest and histone H3 acetylation‐mediated p21WAF1/CIP1 expression
Authors: Tseng Tsui‐Hwa , Chien Ming‐Hsien , Lin Wea‐Lung , Wen Yu‐Ching , Chow Jyh‐Ming , Chen Chi‐Kuan , Kuo Tsang‐Chih , Lee Wei‐Jiunn
Published: February 2016

Apigenin (4′,5,7‐trihydroxyflavone), a flavonoid commonly found in fruits and vegetables, has anticancer properties in various malignant cancer cells. However, the molecular basis of the anticancer effect remains to be elucidated. In this study, we investigated the cellular mechanisms underlying the induction of cell cycle arrest by apigenin. Our results showed that apigenin at the nonapoptotic induction concentration inhibited cell proliferation and induced cell cycle arrest at the G2/M phase in the MDA‐MB‐231 breast cancer cell line. Immunoblot analysis indicated that apigenin suppressed the expression of cyclin A, cyclin B, and cyclin‐dependent kinase‐1 (CDK1), which control the G2‐to‐M phase transition in the cell cycle. In addition, apigenin upregulated p21WAF1/CIP1 and increased the interaction of p21WAF1/CIP1 with proliferating cell nuclear antigen (PCNA), which inhibits cell cycle progression. Furthermore, apigenin significantly inhibited histone deacetylase (HDAC) activity and induced histone H3 acetylation. The subsequent chromatin immunoprecipitation (ChIP) assay indicated that apigenin increased acetylation of histone H3 in the p21WAF1/CIP1 promoter region, resulting in the increase of p21WAF1/CIP1 transcription. In a tumor xenograft model, apigenin effectively delayed tumor growth. In these apigenin‐treated tumors, we also observed reductions in the levels of cyclin A and cyclin B and increases in the levels of p21WAF1/CIP1 and acetylated histone H3. These findings demonstrate for the first time that apigenin can be used in breast cancer prevention and treatment through epigenetic regulation. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 434–444, 2017.
Evaluating a portable cylindrical bait trap to capture diamondback terrapins in salt marsh
Authors: Henry Paula F. P. , Haramis G. Michael , Day Daniel D.
Published: February 2016

Diamondback terrapins (Malaclemys terrapin) are currently in decline across much of their historical range, and demographic data on a regional scale are needed to identify where their populations are at greatest risk. Because terrapins residing in salt marshes are difficult to capture, we designed a cylindrical bait trap (CBT) that could be deployed in shallow tidal waters. From 2003 to 2006, trials were conducted with CBTs in the Chesapeake Bay, Maryland (USA) to determine terrapin sex, size, and age distribution within 3 salt marsh interior habitats—open bays, tidal guts, and broken marshes—using 15 traps/habitat. Analyses based on 791 total captures with CBTs indicate that smaller terrapins, (i.e., adult male and subadult) were more prevalent within the transecting tidal guts and broken marshes, whereas the adult females were more evenly distributed among habitats, including open bays. Subadult females made up the largest percent of catch in the CBTs deployed within the 3 marsh interior habitats. During a 12‐day trial in which we compared capture performance of CBTs and modified fyke nets along open shorelines during the nesting season, fyke nets outperformed CBTs by accounting for 95.2% of the 604 terrapin captures. Although the long drift leads of the fyke nets proved more effective for intercepting along‐shore travel of adult female terrapins during the nesting season, CBTs provided a more effective means of live‐trapping terrapins within the shallow interior marshes. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.
A comparison of acoustic monitoring methods for common anurans of the northeastern United States
Authors: Brauer Corinne L. , Donovan Therese M. , Mickey Ruth M. , Katz Jonathan , Mitchell Brian R.
Published: February 2016

Many anuran monitoring programs now include autonomous recording units (ARUs). These devices collect audio data for extended periods of time with little maintenance and at sites where traditional call surveys might be difficult. Additionally, computer software programs have grown increasingly accurate at automatically identifying the calls of species. However, increased automation may cause increased error. We collected 435 min of audio data with 2 types of ARUs at 10 wetland sites in Vermont and New York, USA, from 1 May to 1 July 2010. For each minute, we determined presence or absence of 4 anuran species (Hyla versicolor, Pseudacris crucifer, Anaxyrus americanus, and Lithobates clamitans) using 1) traditional human identification versus 2) computer‐mediated identification with software package, Song Scope® (Wildlife Acoustics, Concord, MA). Detections were compared with a data set consisting of verified calls in order to quantify false positive, false negative, true positive, and true negative rates. Multinomial logistic regression analysis revealed a strong (P < 0.001) 3‐way interaction between the ARU recorder type, identification method, and focal species, as well as a trend in the main effect of rain (P = 0.059). Overall, human surveyors had the lowest total error rate (<2%) compared with 18–31% total errors with automated methods. Total error rates varied by species, ranging from 4% for A. americanus to 26% for L. clamitans. The presence of rain may reduce false negative rates. For survey minutes where anurans were known to be calling, the odds of a false negative were increased when fewer individuals of the same species were calling. Published 2016. This article is a U.S. Government work and is in the public domain in the USA.