bluuebunny/crossref_metadata_2025 huggingface dataset:
Biopsy Proven Medullary Sponge Kidney: Clinical Findings, Histopathology, and Role of Osteogenesis in Stone and Plaque Formation
Authors: Evan Andrew P. , Worcester Elaine M. , Williams James C. , Sommer Andre J. , Lingeman James E. , Phillips Carrie L. , Coe Fredric L.
Published: January 2015

Medullary sponge kidney (MSK) is associated with recurrent stone formation, but the clinical phenotype is unclear because patients with other disorders may be incorrectly labeled MSK. We studied 12 patients with histologic findings pathognomonic of MSK. All patients had an endoscopically recognizable pattern of papillary malformation, which may be segmental or diffuse. Affected papillae are enlarged and billowy, due to markedly enlarged inner medullary collecting ducts (IMCD), which contain small, mobile ductal stones. Patients had frequent dilation of Bellini ducts, with occasional mineral plugs. Stones may form over white (Randall's) plaque, but most renal pelvic stones are not attached, and have a similar morphology as ductal stones, which are a mixture of calcium oxalate and apatite. Patients had no abnormalities of urinary acidification or acid excretion; the most frequent metabolic abnormality was idiopathic hypercalciuria. Although both Runx2 and Osterix are expressed in papillae of MSK patients, no mineral deposition was seen at the sites of gene expression, arguing against a role of these genes in this process. Similar studies in idiopathic calcium stone formers showed no expression of these genes at sites of Randall's plaque. The most likely mechanism for stone formation in MSK appears to be crystallization due to urinary stasis in dilated IMCD with subsequent passage of ductal stones into the renal pelvis where they may serve as nuclei for stone formation. Anat Rec, 298:865–877, 2015. © 2015 Wiley Periodicals, Inc.
Ontogeny of the Early Triassic Cynodont Thrinaxodon liorhinus (Therapsida): Cranial Morphology
Authors: Jasinoski Sandra C. , Abdala Fernando , Fernandez Vincent
Published: January 2015

The cranial morphology of 68 Thrinaxodon liorhinus specimens, ranging in size from 30 to 96 mm in basal skull length, is investigated using both qualitative and quantitative analyses. From this comprehensive survey, we determined that nine cranial features, including five in the temporal region, separated the sample into four ontogenetic stages. A bivariate analysis of 60 specimens indicated that the skull generally increased in size isometrically, with the exception of four regions. The orbit had negative allometry, a result consistent with other ontogenetic studies of tetrapods, whereas the length of the snout, palate, and temporal region showed positive allometry. The last trend had strong positive allometry indicating that during ontogeny the length of the sagittal crest increased at a much faster rate than the rest of the skull. The large number of changes in the temporal region of the skull of Thrinaxodon may indicate a greater development of the posterior fibres of the temporalis musculature from an early ontogenetic stage. For example, the posterior sagittal crest developed much earlier in ontogeny than the anterior crest that formed in adults, and bone was deposited dorsally creating a unified posterior sagittal crest rather than having a suture that spanned the entire depth of the skull roof. In combination with the isometric height of the zygomatic arch and the almost complete absence of the zygomatic arch angulation, these ontogenetic changes suggest that there was greater development of the temporalis relative to the masseter muscles, indicating a strong posterodorsal movement of the mandible in Thrinaxodon. Anat Rec, 298:1440–1464, 2015. © 2015 Wiley Periodicals, Inc.
A Versatile Platform of 2‐(3,4‐Dihydroxyphenyl) Pyrrolidine Grafted Graphene for Preparation of Various Graphene‐derived Materials
Authors: Zhao Shuai , Wang Haining , Xin Lanxia , Cui Jian , Yan Yehai
Published: January 2015

Covalent functionalization has proven an effective solution for graphene to realize its revolutionary potential in real applications, whereas the platform strategy (a reactive graphene‐based material acting as the platform to undergo post‐reactions for generation of various graphene‐derived materials) is an attractive option to execute efficiently such a task. This contribution demonstrates that 2‐(3,4‐dihydroxyphenyl) pyrrolidine (DHPP) grafted graphene, G‐OH, is a competent platform. Four typical but not exclusive graphene‐derived materials have been prepared from G‐OH by using the chemical virtue of each DHPP unit having three categories totaling six reactive sites. The controlled feature of 1,3‐dipolar cycloaddition for the synthesis of G‐OH ensures that the electronic structure and properties of pristine graphene are succeeded largely by G‐OH and thus its derivatives. A promising alternative to graphene oxide, which has been widely used as a platform to prepare the graphene‐derived materials but suffers from some intrinsic disadvantages, is thus developed.
Investigating the applicability of exclusive pedestrian phase at two‐phase actuated controlled intersections
Authors: Ma Wanjing , Han Baoxin , An Kun , Zhang Nan
Published: January 2015

The exclusive pedestrian phase (EPP) has been used in many countries to promote walking around downtown areas by increasing the ease and convenience of pedestrian crossing. However, its applicability has not been systematically demonstrated, especially when an intersection is operated in actuated mode. This paper presents an extensive simulation‐based analysis of the applicability of EPP as compared with a normal concurrent pedestrian‐phase pattern at an isolated intersection controlled by actuated logic. Actuated signal control logics for EPP‐actuated and conventional concurrent pedestrian phase‐actuated controls are developed. Both of these control logics consider pedestrian crossing demands and can adapt to changes in vehicle traffic to reduce vehicle delay as well. A simulation model of a two‐phase controlled intersection is built and calibrated based on field data using VISSIM (PTV Planung Transport Verkehr AG in Karlsruhe, Germany). Extensive analysis is conducted to reveal fully the applicable EPP domain in terms of vehicle traffic demand, pedestrian demand, vehicle turning ratio, and pedestrian diagonal crossing ratio. The results show that the performance and applicable domain of EPP are jointly determined by those five factors. EPP significantly outperforms concurrent pedestrian phase if the vehicle turning ratio is greater than 0.6 and the pedestrian diagonal crossing ratio is greater than 0.6. These results can help traffic engineers in choosing the appropriate pedestrian‐phase patterns at actuated signalized intersections. Copyright © 2015 John Wiley & Sons, Ltd.
Lactate production by the mammalian blastocyst: Manipulating the microenvironment for uterine implantation and invasion?
Authors: Gardner David K.
Published: January 2015

The mammalian blastocyst exhibits a high capacity for aerobic glycolysis, a metabolic characteristic of tumours. It has been considered that aerobic glycolysis is a means to ensure a high carbon flux to fulfil biosynthetic demands. Here, alternative explanations for this pattern of metabolism are considered. Lactate creates a microenvironment of low pH around the embryo to assist the disaggregation of uterine tissues to facilitate trophoblast invasion. Further it is proposed that lactate acts as a signalling molecule (especially at the reduced oxygen tension present at implantation) to elicit bioactive VEGF recruitment from uterine cells, to promote angiogenesis. Finally it is suggested that the region of high lactate/low pH created by the blastocyst modulates the activity of the local immune response, helping to create immune tolerance. Consequently, the mammalian blastocyst offers a model to study the role of microenvironments, and how metabolites and pH are used in signalling.
In vitro selection of DNAs with an increased propensity to form small circles
Authors: Rosanio Gabriel , Widom Jonathan , Uhlenbeck Olke C.
Published: January 2015

A protocol was devised to select for DNA molecules that efficiently form circles from a library of 126 base pair DNAs containing 90 randomized base pairs. After six rounds of selection, individual molecules from the library showed 20‐ to 100‐fold greater j‐factors compared with the starting library, validating the selection protocol. High‐throughput sequencing revealed a sinusoidal pattern of enrichment and de‐enrichment of A/T dinucleotides in the random region with a 10.4 base pair period associated with the helicity of DNA. A similar, but more moderate pattern of C/G dinucleotides was offset by precisely half a helical turn. While C/G dinucleotide enrichments were evenly distributed, A/T dinucleotide enrichments displayed a preference to cluster in individual DNA molecules. The most highly enriched 10 base pair sequences in the random region contained adjacent blocks of A/T and C/G trinucleotides present in some, but not all, rapidly cyclizing molecules. The phased dinucleotide enrichments closely match those present in accurately mapped yeast nucleosomes, confirming the importance of DNA bending in nucleosome formation. However, at certain sites the nucleosomal DNAs show dinucleotide enrichments that differ substantially from the cyclization data. These discrepancies can often be correlated with sequence specific contacts that form between histones and DNA. © 2015 Wiley Periodicals, Inc. Biopolymers 103: 303–320, 2015.
Uptake and cellular distribution of nucleolar targeting peptides (NrTPs) in different cell types
Authors: Rodrigues Margarida , Andreu David , Santos Nuno C.
Published: January 2015

Nucleolar targeting peptides (NrTPs) are a family of cell penetrating peptides (CPPs) derived from crotamine, a rattlesnake venom toxin. They were named NrTPs for their remarkable nucleolus‐homing properties and have been studied for their potential as drug delivery vehicles. Live cell microscopy experiments were conducted to monitor NrTP uptake and distribution in different cell types, including primary cells (PBMCs and erythrocytes) and different immortalized cell lines (HeLa, BHK21, BV‐173, and MOLT‐4). Uptake dependence on cell type (primary vs. immortalized, suspension vs. adherent, cancer vs. healthy cells), peptide concentration and cell viability were evaluated. To gain further insight on the internalization mechanism, uptake kinetics was also monitored. Results showed the uptake and distribution pattern as strongly dependent on peptide sequence, peptide concentration and membrane constituents. Under similar conditions, NrTP6 is more internalized than NrTP1, NrTP2 and NrTP5. Additionally, while internalization of NrTP7 and NrTP8 may cause cytotoxicity, NrTP6 is noncytotoxic. Higher peptide concentrations can be correlated to nucleolar targeting, although even at low concentrations a residual number of cells reveal positive nucleolar labeling. NrTPs were successfully internalized into all cell types tested except erythrocytes. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 104: 101–109, 2015.
Shear‐Stress‐Mediated Refolding of Proteins from Aggregates and Inclusion Bodies
Authors: Yuan Tom Z. , Ormonde Callum F. G. , Kudlacek Stephan T. , Kunche Sameeran , Smith Joshua N. , Brown William A. , Pugliese Kaitlin M. , Olsen Tivoli J. , Iftikhar Mariam , Raston Colin L. , Weiss Gregory A.
Published: January 2015

Recombinant protein overexpression of large proteins in bacteria often results in insoluble and misfolded proteins directed to inclusion bodies. We report the application of shear stress in micrometer‐wide, thin fluid films to refold boiled hen egg white lysozyme, recombinant hen egg white lysozyme, and recombinant caveolin‐1. Furthermore, the approach allowed refolding of a much larger protein, cAMP‐dependent protein kinase A (PKA). The reported methods require only minutes, which is more than 100 times faster than conventional overnight dialysis. This rapid refolding technique could significantly shorten times, lower costs, and reduce waste streams associated with protein expression for a wide range of industrial and research applications.
Specialist Periodical Reports: Synthetic Biology Vol. 1. Edited by Maxim Rydanov, Luc Brunsveld and Hiroaki Suga.
Authors: Maiti Souvik
Published: January 2015

RSC, Cambridge 2014, XV+359 pp., hardcover, £ 314.95.—ISBN 978‐1‐84973‐683‐1
At a crossroads: An Amulet in the uneasy left atrial appendage crown
Authors: Turi Zoltan G.
Published: January 2015

Key Points

This is a small but well‐presented series describing a second generation Amplatzer Cardiac Plug device with short‐term follow‐up.

As with the first generation device, a high level evidence base remains lacking.

Left atrial appendage occlusion is at a crossroads, exacerbated by years of ad hoc use of a variety of such technologies that, other than the WATCHMAN, have not been subjected to randomized controlled studies.
Left atrial appendage closure—facing the truth and forging the future
Authors: Eng Marvin H. , Price Matthew J.
Published: January 2015

Key Points

Computed tomography almost doubles the detection of peri‐device leaks compared to trans‐esophageal echocardiography post‐Amplatzer Occluder Plug implantation.

Oversizing at least 10% of the appendage orifice may be a helpful parameter in minimizing peri‐device leak.

The significance of residual leaks remains unclear.
Nanocrystalline M–MOF‐74 as Heterogeneous Catalysts in the Oxidation of Cyclohexene: Correlation of the Activity and Redox Potential
Authors: Ruano Daniel , Díaz‐García Manuel , Alfayate Almudena , Sánchez‐Sánchez Manuel
Published: January 2015

In some aspects, the potential of metal–organic framework (MOF) materials as heterogeneous catalysts has been realized, at least in an academic context. However, one of their most promising catalytic properties, that is, the presence of open metal sites, is far from understood properly. In this work, a series of M–MOF‐74 (M=Mn, Co, Ni, Cu, Zn) materials, prepared under sustainable conditions, was tested systematically in the oxidation of cyclohexene, which can proceed by either radical or epoxidation routes. Under the optimized reaction conditions, the radical route is spontaneous to some extent and it is enhanced in the presence of any M–MOF‐74 that has a metal with a redox character but not Zn. However, the epoxidation of cyclohexene is also promoted by a redox catalyst in such a way that the conversion correlates qualitatively with the redox potential of the metal. Thus, for the first time, a chemical property of M is correlated with the catalytic activity of the M–MOF‐74 family.
Optimization of Design and Performance of Solid‐Liquid Separators: A Thickener Hydrocyclone
Authors: Silva Danylo O. , Vieira Luiz G. M. , Barrozo Marcos A. S.
Published: January 2015

Studies on hydrocyclones have evolved over recent years and various configurations of this device have been proposed in the literature for different purposes. Herein, an innovative geometrical configuration of hydrocyclones was developed by means of the response surface technique, combined with an optimization algorithm and supported by a computational fluid dynamics complementary study. The results obtained with these optimization techniques were validated by experimental data. The optimized hydrocyclone configuration is characterized by low energy consumption, i.e., low Euler number, with a small underflow‐to‐throughput ratio and can be used as a thickener hydrocyclone.
Application of Strong Porous Polymer Sheets for Superior Oil Spill Recovery
Authors: Saleem Junaid , Bazargan Alireza , Barford John , McKay Gordon
Published: January 2015

The usage of natural and synthetic sorbents in order to control oil spills is gaining increasing attention due to environmental concerns. In particular, polyolefins including polypropylene and polyethylene are the most commonly used oil sorbent materials because of their low cost but suffer from low oil absorption capacity. Attempts at trying to increase the surface‐to‐thickness ratio for improving uptake capacity makes them vulnerable to breakage and impractical for most oil spill applications. Novel super oil sorbent polymer sheets consisting of porous ultrahigh‐molecular‐weight polyethylene have been prepared. The presented sorbent exhibits extremely high uptake and retention capacities along with a mechanically strong structure. The combination of these factors as well as the cost effectiveness of the material used makes these sheets viable candidates for widespread production and utilization.
Metal‐halide Nanoparticle Formation: Electrolytic and Chemical Synthesis of Mercury(I) Chloride Nanoparticles
Authors: Bartlett Thomas R. , Batchelor‐McAuley Christopher , Tschulik Kristina , Jurkschat Kerstin , Compton Richard G.
Published: January 2015

Mercury(I) chloride (Hg2Cl2) nanoparticles (NPs) are synthesised for the first time by using two different techniques. First, particles are formed by implosion of a calomel nanolayer, induced by partial electrolysis at a mercury hemisphere microelectrode. The resulting NPs are then characterised by the nanoimpact method, demonstrating the first time metal chloride NPs have been sized by this technique and showing the ability to form and study NPs in situ. Second, Hg2Cl2 NPs are synthesised by using the precipitation reaction of Hg2(NO3)2 with KCl. The NPs are characterised on both mercury and carbon microelectrodes and their size is found to agree with TEM results.
Broad Hexagonal Columnar Mesophases Formation in Bioinspired Transition‐Metal Complexes of Simple Fatty Acidmeta‐Octaester Derivatives ofmeso‐Tetraphenyl Porphyrins
Authors: Wu Bin , Chen Keyang , Deng Yuchen , Chen Jian , Liu Chengjie , Cheng Rongshi , Chen Dongzhong
Published: January 2015

A series ofmeta‐substituted fatty acid octaester derivatives and their transition‐metal complexes ofmeso‐ tetraphenyl porphyrins (TPP‐8OOCR, with R=Cn−1H2n−1,n=8, 12, or 16) have been prepared through very simple synthesis protocols. The thermotropic phase behavior and the liquid crystalline (LC) organization structures of the synthesized porphyrin derivatives were systematically investigated by a combination of differential scanning calorimetry (DSC), polarized optical microscopy (POM), and variable‐temperature small‐angle X‐ray scattering/wide‐angle X‐ray scattering (SAXS/WAXS) techniques. The shorter octanoic acid ester substituted porphyrin (C8‐TPP) did not show liquid crystallinity and its metal porphyrins exhibited an uncommon columnar mesophase. The lauric acid octaester (C12‐TPP) and the palmitic acid octaester (C16‐TPP) series porphyrins generated hexagonal columnar mesophase Colh. Moreover, the metal porphyrins C12‐TPPM and C16‐TPPM with M=Zn, Cu, or Ni, exhibited well‐organized Colhmesophases of broad LC temperature ranges increasing in the order of TPPNi<TPPCu≤TPPZn with their increased effective ionic radii in the square‐planar coordination. The simplicity in synthesis, the well intercolumnar organization of Colhmesophase, the broadness of the discotic LC range, and the specific UV/Vis absorption and fluorescence emission behaviors make the symmetrically substituted fatty acid octaester porphyrins and their metal complexes very attractive for variant applications.
Dual Gold‐Catalyzed Head‐to‐Tail Coupling of Iodoalkynes
Authors: Mader Steffen , Molinari Lise , Rudolph Matthias , Rominger Frank , Hashmi A. Stephen K.
Published: January 2015

Various haloalkynes are converted in the presence of a dual activation gold catalyst. Via a dual activation process a completely atom economic head‐to‐tail coupling delivers gem‐dihalogenated conjugated enynes as valuable building blocks for organic synthesis.
Structuring of Reactors and Catalysts on Multiple Scales: Potential and Limitations for Fischer‐Tropsch Synthesis
Authors: Güttel Robert
Published: January 2015

Structuring of catalysts and reactors increases the number of degrees of freedom and thus allows tailoring the design for each particular application. Thereby, transport processes can be intensified in order to increase the reactor productivity. This contribution illustrates concepts of structuring on different lengths scales for Fischer‐Tropsch synthesis as example. On this basis the approach of multi‐scale structuring is proposed in order to achieve an improved control of transport processes in chemical reactors.
The catalytic domain of inositol‐1,4,5‐trisphosphate 3‐kinase‐a contributes to ITPKA‐induced modulation of F‐actin
Authors: Ashour Dina Julia , Pelka Benjamin , Jaaks Patricia , Wundenberg Torsten , Blechner Christine , Zobiak Bernd , Failla Antonio Virgilio , Windhorst Sabine
Published: January 2015

Inositol‐1,4,5‐trisphosphate‐3‐kinase‐A (ITPKA) has been considered as an actin bundling protein because its N‐terminal actin binding domain (ABD) induces formation of linear actin bundles. Since in many cancer cell lines ITPKA is essential for formation of lamellipodia, which consist of cross‐linked actin filaments, here we analyzed if full length‐ITPKA may induce formation of more complex actin structures. Indeed, we found that incubation of F‐actin with ITPKA resulted in formation of dense, branched actin networks. Based on our result that ITPKA does not exhibit an additional C‐terminal ABD, we exclude that ITPKA cross‐links actin filaments by simultaneous F‐actin binding with two different ABDs. Instead, stimulated‐emission‐depletion‐microscopy and measurement of InsP3Kinase activity give evidence that that N‐terminal ABD‐homodimers of ITPKA bind to F‐actin while the monomeric C‐termini insert between adjacent actin filaments. Thereby, they prevent formation of thick actin bundles but induce formation of thin branched actin structures. Interestingly, when embedded in this dense actin network, InsP3Kinase activity is doubled and the product of InsP3Kinase activity, Ins(1,3,4,5)P4, inhibits spontaneous actin polymerization which may reflect a local negative feedback regulation of InsP3Kinase activity. In conclusion, we demonstrate that not only the ABD of ITPKA modulates actin dynamics but reveal that the InsP3Kinase domain substantially contributes to this process. © 2015 Wiley Periodicals, Inc.
Moniliform deformation of retinal ganglion cells by formaldehyde‐based fixatives
Authors: Stradleigh Tyler W. , Greenberg Kenneth P. , Partida Gloria J. , Pham Aaron , Ishida Andrew T.
Published: January 2015

Protocols for characterizing cellular phenotypes commonly use chemical fixatives to preserve anatomical features, mechanically stabilize tissue, and stop physiological responses. Formaldehyde, diluted in either phosphate‐buffered saline or phosphate buffer, has been widely used in studies of neurons, especially in conjunction with dyes and antibodies. However, previous studies have found that these fixatives induce the formation of bead‐like varicosities in the dendrites and axons of brain and spinal cord neurons. We report here that these formaldehyde formulations can induce bead formation in the dendrites and axons of adult rat and rabbit retinal ganglion cells, and that retinal ganglion cells differ from hippocampal, cortical, cerebellar, and spinal cord neurons in that bead formation is not blocked by glutamate receptor antagonists, a voltage‐gated Na+ channel toxin, extracellular Ca2+ ion exclusion, or temperature shifts. Moreover, we describe a modification of formaldehyde‐based fixatives that prevents bead formation in retinal ganglion cells visualized by green fluorescent protein expression and by immunohistochemistry. J. Comp. Neurol. 523:545–564, 2015. © 2014 Wiley Periodicals, Inc.
Color prediction models for digital Jacquard woven fabrics
Authors: Chae Youngjoo , Xin John H. , Hua Tao
Published: January 2015

The current industry practice for producing jacquard fabrics uses computer‐aided design (CAD) systems that provide visual simulations of the final color appearance of actual fabrics prior to production. This digital process is fundamentally based on the prediction of combined weave‐color effects, which can be successfully achieved by accurate color mixing models and the structural details of the fabrics. With the accurate models used in CAD systems, designers would see simulations more closely resembling fabrics to be produced. By checking the previews, the designers can easily modify, that is, recolor, the designs on the display monitor without doing repetitive physical sampling with the adjustment of the weaves and the yarn colors. However, there is no ready applicable accurate color mixing model for woven structures and there has not been sufficient investigation of the color prediction despite its usefulness for the current digital CAD process. Our study investigated the, color prediction of jacquard woven fabrics designed based on the principle of optically subtractive color mixing with the use of CMY colors. The color prediction was firstly done through the application of the six color mixing models previously developed for various other applications including fiber blending and printing. The performance of each model was evaluated by calculating the difference between the predicted and the measured colorimetric data, using ΔECMC(2:1). The average color difference from the models was 11.93 ΔECMC(2:1), which is hardly acceptable in textile industry. In order to increase the accuracy in color prediction, the six models were then optimized. As a result, substantial improvements for all models were obtained with a decrease in color difference to 4.83 ΔECMC(2:1)on average after the optimizations. Among the six optimized color mixing models, the optimized Warburton‐Oliver model, that is, W‐O model, was found to have the lowest average ΔECMC(2:1)value of approximately equaling to 2, which is considered potentially useful to be applied to the current digital fabric color prediction. © 2015 Wiley Periodicals, Inc. Col Res Appl, 41, 64–71, 2016
Conjugated Polymer–Porphyrin Complexes for Organic Electronics
Authors: Andernach Rolf E. , Rossbauer Stephan , Ashraf Raja S. , Faber Hendrik , Anthopoulos Thomas D. , McCulloch Iain , Heeney Martin , Bronstein Hugo A.
Published: January 2015

We present the synthesis of novel conjugated polymer–porphyrin complexes for use in organic electronics. Linear and star‐shaped platinated porphyrins were attached to regioregular poly(3‐hexylthiophene‐2,5‐diyl) (P3HT) arms to investigate whether porphyrin stacking and increased dimensionality can be used to control polymer morphology. The novel materials display similar optical properties to P3HT, but give higher mobilities when used in organic field‐effect transistors. Atomic force microscopy measurements show that incorporation of only a small amount of porphyrin into the conjugated polymer backbone leads to increased aggregation. These materials demonstrate that polymer morphology and performance can be tuned and enhanced effectively through the use of conjugatively linked porphyrins.
Pressure in electronically excited warm dense metals
Authors: Stegailov V. , Zhilyaev P.
Published: January 2015

Non‐equilibrium two‐temperature warm dense metals consist of the ion subsystem that is subjected to structural transitions and involved in the mass transfer, and the electron subsystem that in various pulsed experiments absorbs energy and then evolves together with ions to equilibrium. Definition of pressure in such non‐equilibrium systems causes certain controversy. In this work we make an attempt to clarify this definition that is vital for proper description of the whole relaxation process. Using the density functional theory we analyze on examples of Al and Au electronic pressure components in warm dense metals. Appealing to the Fermi gas model we elucidate a way to find a number of free delocalized electrons in warm dense metals. (© 2015 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Semiautomated analysis of embryoscope images: Using localized variance of image intensity to detect embryo developmental stages
Authors: Mölder Anna , Drury Sarah , Costen Nicholas , Hartshorne Geraldine M. , Czanner Silvester
Published: January 2015

Embryo selection in in vitro fertilization (IVF) treatment has traditionally been done manually using microscopy at intermittent time points during embryo development. Novel technique has made it possible to monitor embryos using time lapse for long periods of time and together with the reduced cost of data storage, this has opened the door to long‐term time‐lapse monitoring, and large amounts of image material is now routinely gathered. However, the analysis is still to a large extent performed manually, and images are mostly used as qualitative reference. To make full use of the increased amount of microscopic image material, (semi)automated computer‐aided tools are needed. An additional benefit of automation is the establishment of standardization tools for embryo selection and transfer, making decisions more transparent and less subjective. Another is the possibility to gather and analyze data in a high‐throughput manner, gathering data from multiple clinics and increasing our knowledge of early human embryo development. In this study, the extraction of data to automatically select and track spatio‐temporal events and features from sets of embryo images has been achieved using localized variance based on the distribution of image grey scale levels. A retrospective cohort study was performed using time‐lapse imaging data derived from 39 human embryos from seven couples, covering the time from fertilization up to 6.3 days. The profile of localized variance has been used to characterize syngamy, mitotic division and stages of cleavage, compaction, and blastocoel formation. Prior to analysis, focal plane and embryo location were automatically detected, limiting precomputational user interaction to a calibration step and usable for automatic detection of region of interest (ROI) regardless of the method of analysis. The results were validated against the opinion of clinical experts. © 2015 International Society for Advancement of Cytometry
Anaplastic thyroid carcinoma with rhabdoid features
Authors: Feng Gong , Laskin William B. , Chou Pauline M. , Lin Xiaoqi
Published: January 2015

Anaplastic thyroid carcinoma (ATC) is a rare, highly aggressive neoplasm, characterized by complete or partial composition by undifferentiated cells. We report a case of ATC with rhabdoid features in a 68‐year‐old male, who presented with a rapidly enlarging neck mass. Fine‐needle aspiration (FNA) of the thyroid mass showed discohesive, pleomorphic round to polygonal rhabdoid cells with one to multiple eccentric, large, rounded nuclei with a prominent nucleolus, moderate to abundant, globoid cytoplasm which oftentimes harbor a pale para‐nuclear inclusion. The cytoplasm of some cells contained variously sized, eosinophilic granules. Rare cells contained neutrophils in their cytoplasm. Mitoses including atypical mitotic figures and necrosis were readily seen. Histologic examination of needle core biopsy (NCB) revealed individual dispersed and sheets of pleomorphic neoplastic cells with similar cytomorphologic features as described above. The tumor extensively infiltrated a myxocollagenous stroma containing lymphocytes and neutrophils, and demonstrated foci of necrosis. Tumor cells were immunoreactive for keratins AE1/AE3, CAM5.2, and CK19; PAX‐8, and p63, but negative for S‐100, HMB‐45, calcitonin, TTF‐1, thyroglobulin, CD56, HBME‐1, glypican‐3, PAX‐5, myogenin, CD31, and INI‐1. The differential diagnosis of this malignant rhabdoid tumor is discussed. Diagn. Cytopathol. 2015;43:416–420. © 2015 Wiley Periodicals, Inc.
Diagnostic problems of salivary gland tumors
Authors: Tyagi Ruchita , Dey Pranab
Published: January 2015

Fine needle aspiration cytology (FNAC) of salivary gland is a popular technique with high sensitivity and specificity. However, the interpretation of FNAC smear of salivary gland lesions is a great challenge to the cytologists. The cytological features of the various tumors of the salivary gland have overlapping cytological features and many other lesions in the head neck region may mimic salivary lesions. Moreover, at times it may be difficult to differentiate benign from malignant tumor of the tumor with same cell of origin. In this article, we have discussed the various problems in the diagnosis of FNAC of the salivary gland lesions. Diagn. Cytopathol. 2015;43:495–509. © 2015 Wiley Periodicals, Inc.
Plant diversity and identity effects on predatory nematodes and their prey
Authors: Kostenko Olga , Duyts Henk , Grootemaat Saskia , De Deyn Gerlinde B. , Bezemer T. Martijn
Published: January 2015

There is considerable evidence that both plant diversity and plant identity can influence the level of predation and predator abundance aboveground. However, how the level of predation in the soil and the abundance of predatory soil fauna are related to plant diversity and identity remains largely unknown. In a biodiversity field experiment, we examined the effects of plant diversity and identity on the infectivity of entomopathogenic nematodes (EPNs, Heterorhabditis and Steinernema spp.), which prey on soil arthropods, and abundance of carnivorous non‐EPNs, which are predators of other nematode groups. To obtain a comprehensive view of the potential prey/food availability, we also quantified the abundance of soil insects and nonpredatory nematodes and the root biomass in the experimental plots. We used structural equation modeling (SEM) to investigate possible pathways by which plant diversity and identity may affect EPN infectivity and the abundance of carnivorous non‐EPNs. Heterorhabditis spp. infectivity and the abundance of carnivorous non‐EPNs were not directly related to plant diversity or the proportion of legumes, grasses and forbs in the plant community. However, Steinernema spp. infectivity was higher in monocultures of Festuca rubra and Trifolium pratense than in monocultures of the other six plant species. SEM revealed that legumes positively affected Steinernema infectivity, whereas plant diversity indirectly affected the infectivity of Heterorhabditis EPNs via effects on the abundance of soil insects. The abundance of prey (soil insects and root‐feeding, bacterivorous, and fungivorous nematodes) increased with higher plant diversity. The abundance of prey nematodes was also positively affected by legumes. These plant community effects could not be explained by changes in root biomass. Our results show that plant diversity and identity effects on belowground biota (particularly soil nematode community) can differ between organisms that belong to the same feeding guild and that generalizations about plant diversity effects on soil organisms should be made with great caution.
On the use of stable oxygen isotope (δ18O) measurements for tracking avian movements in North America
Authors: Hobson Keith A. , Koehler Geoff
Published: January 2015

Tracking migratory animals has benefitted using measurements of naturally occurring stable isotopes of hydrogen (δ2H) in keratinous tissues such as hair and feathers to link animal origins to continental patterns or isoscapes of δ2H in precipitation. However, for most taxa, much less information exists on the use of stable oxygen isotope ratios (δ18O) despite the fact that δ2H and δ18O are strongly linked in environmental waters through the meteoric relationship and the possibility of using both isotopes to infer greater information on origins and climatic conditions where tissues are grown. A fundamental requirement of using stable isotopes to assign individuals and populations to origins is the development of a rescaling function linking environmental food web signals to the tissue of interest and for birds, this has not been carried out. Here, we derived the relationship between H and O isotopes in known source feathers of 104 individuals representing 11 species of insectivorous passerines sampled across the strong precipitation isoscape of North America. We determined again a strong expected relationship between feather δ2H (δ2Hf) and long‐term amount‐weighted precipitation δ2H (δ2Hp; r2 = 0.77), but the corresponding relationship between δ18Of and δ18Op was poor (r2 = 0.32) for the same samples. This suggests that δ2H measurements are currently more useful for assignment of insectivorous songbirds to precipitation isoscapes but does not preclude other uses of the δ18Of data. Currently, mechanisms responsible for the decoupling of H and O isotopes in food webs is poorly known, and we advocate a much broader sampling of both isotopes in the same keratinous tissues across precipitation isotope gradients and across taxa to resolve this issue and to increase the power of using water isotopes to track migratory animals.
Limited sampling hampers “big data” estimation of species richness in a tropical biodiversity hotspot
Authors: Engemann Kristine , Enquist Brian J. , Sandel Brody , Boyle Brad , Jørgensen Peter M. , Morueta‐Holme Naia , Peet Robert K. , Violle Cyrille , Svenning Jens‐Christian
Published: January 2015

Macro‐scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample‐size‐correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species‐rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second‐order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with “big data” collections.
Short‐term resilience of arthropod assemblages after spring flood, with focus on spiders (Arachnida: Araneae) and carabids (Coleoptera: Carabidae)
Authors: Lafage Denis , Sibelle Charlotte , Secondi Jean , Canard Alain , Pétillon Julien
Published: January 2015

Despite the expected increase in extreme flood frequency, the manner in which terrestrial arthropods cope with regular submersion of their habitat remains poorly understood in meadows, especially in temperate floodplains. Here, we studied the recolonization dynamics of arthropods after a severe spring flood in the Loire Valley (France). We carried out analyses at the community (order or family identification level) and species scales, focusing on the assemblages of two dominant and diverse groups: carabids and spiders. Our objectives were the following: (i) to describe the temporal changes in community structure after flooding and (ii) to assess the influence of landscape configuration on recolonization patterns of species and their functional traits. Fieldwork was performed along three sampling transects, by using 75 pitfall traps, in 2012. A total of 14 767 arthropods belonging to 87 families were trapped, including 5538 spiders (55 species) and 3396 carabids (66 species). Multivariate analyses discriminated assemblages from flooded and non‐flooded habitats and revealed changes over time in arthropod families and species after flood withdrawal. In particular, wolf spiders (Lycosidae) were the first to recolonize, whereas other groups clearly avoided flooded sites. Our results also revealed that short distances to hedgerows, and to a lesser extent, distance to woodlands, favoured the recolonization of large and ground‐running spiders. In conclusion, our study shows the short‐term resilience of certain groups or stenotopic species to flooding and also the relevance of multi‐taxon‐based studies. The presence of hedgerows has to be considered carefully in management plans because of their role of refuge during flooding. Copyright © 2015 John Wiley & Sons, Ltd.
B cells expressing IFN‐γ suppress Treg‐cell differentiation and promote autoimmune experimental arthritis
Authors: Olalekan Susan A. , Cao Yanxia , Hamel Keith M. , Finnegan Alison
Published: January 2015

Clinical efficacy in the treatment of rheumatoid arthritis with anti‐CD20 (Rituximab)‐mediated B‐cell depletion has garnered interest in the mechanisms by which B cells contribute to autoimmunity. We have reported that B‐cell depletion in a murine model of proteoglycan‐induced arthritis (PGIA) leads to an increase in Treg cells that correlate with decreased autoreactivity. Here, we demonstrate that the increase in Treg cells after B‐cell depletion is due to an increase in the differentiation of naïve CD4+ T cells into Treg cells. Since the development of PGIA is dependent on IFN‐γ and B cells are reported to produce IFN‐γ, we hypothesized that B‐cell‐specific IFN‐γ plays a role in the development of PGIA. Accordingly, mice with B‐cell‐specific IFN‐γ deficiency were as resistant to the induction of PGIA as mice that were completely IFN‐γ deficient. Importantly, despite a normal frequency of IFN‐γ‐producing CD4+ T cells, B‐cell‐specific IFN‐γ‐deficient mice exhibited a higher percentage of Treg cells compared with that in WT mice. These data indicate that B‐cell IFN‐γ production inhibits Treg‐cell differentiation and exacerbates arthritis. Thus, we have established that IFN‐γ, specifically derived from B cells, uniquely contributes to the pathogenesis of autoimmunity through prevention of immunoregulatory mechanisms.
F pocket flexibility influences the tapasin dependence of two differentially disease‐associated MHC Class I proteins
Authors: Abualrous Esam T. , Fritzsche Susanne , Hein Zeynep , Al‐Balushi Mohammed S. , Reinink Peter , Boyle Louise H. , Wellbrock Ursula , Antoniou Antony N. , Springer Sebastian
Published: January 2015

The human MHC class I protein HLA‐B*27:05 is statistically associated with ankylosing spondylitis, unlike HLA‐B*27:09, which differs in a single amino acid in the F pocket of the peptide‐binding groove. To understand how this unique amino acid difference leads to a different behavior of the proteins in the cell, we have investigated the conformational stability of both proteins using a combination of in silico and experimental approaches. Here, we show that the binding site of B*27:05 is conformationally disordered in the absence of peptide due to a charge repulsion at the bottom of the F pocket. In agreement with this, B*27:05 requires the chaperone protein tapasin to a greater extent than the conformationally stable B*27:09 in order to remain structured and to bind peptide. Taken together, our data demonstrate a method to predict tapasin dependence and physiological behavior from the sequence and crystal structure of a particular class I allotype.

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Systematic purification of salt‐intolerant proteins by ion‐exchange chromatography: The example of human α‐galactosidase A
Authors: Baumann Pascal , Osberghaus Anna , Hubbuch Jürgen
Published: January 2015

Chromatography is an essential tool for purifying biopharmaceutical products. Many processes are still developed based on traditional routines and empirical procedures. Product losses are mostly due to insufficient optimization of purification setups and product sensitivity to process conditions. In order to eliminate these shortcomings, a systematic strategy for the setup of ion‐exchange chromatography is presented, which considers both product stability as well as operational conditions. The stages—a hybrid approach combining high‐throughput screening and analytical small‐scale chromatography—are as follows: (1) pH stability (short‐term); (2) pH stability (long‐term), followed by a screening of additives to enhance protein stability, if required; (3) analytical pH gradient chromatography for evaluation of the operational pH window; and (4) salt stability (long‐term) in the operational pH window determined. The efficiency and straightforwardness of the strategy were shown in a case study on capturing the human α‐galactosidase A enzyme. Following the above procedure, the enzyme was found to be salt‐unstable; a purification factor of 13.2, a concentration factor of 4, and an overall yield of 84.3% were achieved. The applied strategy allowed for a quick establishment of a dedicated capture step at low salt concentrations under stable conditions by well‐chosen prior screening experiments.
Cyclic Dehydrogenation–(Re)Hydrogenation with Hydrogen‐Storage Materials: An Overview
Authors: Chamoun Rita , Demirci Umit B. , Miele Philippe
Published: January 2015

Hydrogen‐storage materials (HSMs) have especially revolutionized the field of “hydrogen storage” by offering a relatively safe storage alternative and high gravimetric hydrogen density. However, a critical challenge is storage reversibility. This is the central tenet of the present article, which discusses ways to close the hydrogen cycle with solid‐ and liquid‐phase HSMs. A distinction between the different HSMs is made on the basis of the approach under which they can be rehydrogenated; this led to the proposition of distribution in three categories: one, materials allowing reversible storage of H2; two, hydrogen carriers for which the byproducts must be recycled; three, sustainable hydrogen carriers with which the hydrogen cycle is considered as being byproduct free. From our analysis, supported by many examples, it seems that the hydrogen cycle can be closed with all of the HSMs discussed herein and that the dehydrogenation/rehydrogenation paths depend on their nature.
Issues and Challenges for Bulk‐Type All‐Solid‐State Rechargeable Lithium Batteries using Sulfide Solid Electrolytes
Authors: Jung Yoon Seok , Oh Dae Yang , Nam Young Jin , Park Kern Ho
Published: January 2015

As lithium rechargeable batteries are considered a potential candidate for large‐scale energy storage applications in devices such as electric vehicles (EVs) and smart grids, their safety has become of prime concern. This calls for the need to replace the flammable organic liquid electrolyte (LE) with an inorganic solid electrolyte (SE), and thus, develop bulk‐type all‐solid‐state lithium batteries (ASLBs), fabricated using a scalable process. Sulfide SEs are considered the most competitive candidate owing to their high conductivity at room temperature (10−3–10−2 S cm−1), which is comparable to that of LEs, and their ductility, which enables the fabrication of ASLBs simply using cold pressing. In the present review, issues and challenges to be faced for the fabrication of bulk‐type ASLBs using sulfide SEs are presented and discussed, with a special focus on the development of SEs, compatibility of the electrode materials with SEs, and structure of the composite electrodes. Recent progress made with the aim of addressing the aforementioned issues and challenges is also presented, to provide an outlook on the future of SEs and ASLBs.
Recent Development on Anodes for Na‐Ion Batteries
Authors: Bommier Clement , Ji Xiulei
Published: January 2015

New discoveries in anode materials for sodium ion batteries (NIBs) are highly necessary to achieve the goals of widespread applications, such as electric vehicles (EVs) and grid‐level energy storage. Carbon‐based materials are critical for this task as they are inexpensive, abundant, and versatile. They contain a plethora of structures and morphologies, ranging from highly ordered graphite or nanotubes to highly disordered amorphous carbon, thus making them very attractive for electrochemical energy storage. This review attempts to cover past and recent progress in the development of carbon‐based anode materials for NIBs. To give a larger context, the article will briefly cover other anode materials for NIBs as well. The aim of this paper is to provide a timely update for researchers currently involved in the respective fields or to serve as a starting point for individuals who would like to gain a greater knowledge of new NIB anode materials.