bluuebunny/crossref_metadata_2025 huggingface dataset:
Revisiting free school meal eligibility as a proxy for pupil socio‐economic deprivation
Authors: Ilie Sonia , Sutherland Alex , Vignoles Anna
Published: January 2017

Whether someone has ever had free school meal (FSM) eligibility over a six‐year period is the measure of socio‐economic disadvantage currently used in the English school system. It is used to monitor the socio‐economic gap in achievement in the education system, to identify particular children at risk of low achievement and to direct funding to particular children and schools. In this paper we assess how well this measure predicts pupil attainment in secondary school in comparison to other measures of socio‐economic background known to influence pupil attainment, such as parental education or income. We ask whether the FSM measure is an adequate proxy for a pupil's socio‐economic disadvantage in an educational context. To do this we draw on the Longitudinal Study of Young People in England and matched administrative data. We find that the FSM eligibility measure correlates highly with other measures of socio‐economic disadvantage, however it does not identify all children living in what would be deemed deprived households. We then compare the extent to which the FSM eligibility measure predicts educational achievement relative to other measures of deprivation and find that its predictive power is only marginally lower than many richer survey measures. This provides some reassurance on its use in policy.
Log D versus HPLC derived hydrophobicity: The development of predictive tools to aid in the rational design of bioactive peptoids
Authors: Bolt H. L. , Williams C. E. J. , Brooks R. V. , Zuckermann R. N. , Cobb S. L. , Bromley E. H. C.
Published: January 2017

Hydrophobicity has proven to be an extremely useful parameter in small molecule drug discovery programmes given that it can be used as a predictive tool to enable rational design. For larger molecules, including peptoids, where folding is possible, the situation is more complicated and the average hydrophobicity (as determined by RP‐HPLC retention time) may not always provide an effective predictive tool for rational design. Herein, we report the first ever application of partitioning experiments to determine the log D values for a series of peptoids. By comparing log D and average hydrophobicities we highlight the potential advantage of employing the former as a predictive tool in the rational design of biologically active peptoids.
Three-point transfusion risk score in hepatectomy
Authors:   HPB CONCEPT Team, Lemke M , Law C H L , Li J , Dixon E , Tun Abraham M , Hernandez Alejandro R , Bennett S , Martel G , Karanicolas P J
Published: January 2017

Background

Perioperative red blood cell transfusions are required in up to 23 per cent of patients undergoing hepatectomy. Previous research has developed three transfusion risk scores to assess risk of perioperative red blood cell transfusion. Here, the performance of these transfusion risk scores was evaluated in a multicentre cohort of patients who underwent hepatectomy and compared with that of a simplified transfusion risk score.

Methods

A database of patients undergoing hepatectomy at four specialized centres between 2008 and 2012 was developed. External validity was assessed by discrimination and calibration. Discrimination was evaluated using the area under the receiver operating characteristic (ROC) curve (AUC). Calibration was evaluated by the degree of agreement between predicted and actual red blood cell transfusion probabilities. A simplified transfusion risk score using variables common to the three models was created, and discrimination and calibration were evaluated.

Results

There were 1287 patients included in this study, with 341 (26·5 per cent) receiving a red blood cell transfusion. Discriminative ability was similar between the three transfusion risk scores, with AUCs of 0·66–0·68 and good calibration. A new three-point risk score was developed based on factors present in all models: haemoglobin 12·5 g/dl or less, primary liver malignancy and major resection (at least 4 segments). Discriminative ability and calibration of the three-point model were similar to those of the three existing models, with an AUC of 0·66.

Conclusion

The three-point transfusion risk score simplifies assessment of perioperative transfusion risk in hepatectomy without sacrificing predictive ability.
Outcomes of surgical shunts and transjugular intrahepatic portasystemic stent shunts for complicated portal hypertension
Authors: Hosokawa I , Adam R , Allard M-A , Pittau G , Vibert E , Cherqui D , Sa Cunha A , Bismuth H , Miyazaki M , Castaing D
Published: January 2017

Background

Transjugular intrahepatic portasystemic stent shunt (TIPSS), instead of surgical shunt, has become the standard treatment for patients with complicated portal hypertension. This study compared outcomes in patients who underwent TIPSS or surgical shunting for complicated portal hypertension.

Methods

This was a retrospective study of all consecutive patients who received portasystemic shunts from 1994 to 2014 at a single institution. Patients who underwent surgical shunting were compared with those who had a TIPSS procedure following one-to-one propensity score matching. The primary study endpoints were overall survival and shunt failure, defined as major variceal rebleeding, relapse of refractory ascites, irreversible shunt occlusion, liver failure requiring liver transplantation, or death.

Results

A total of 471 patients received either a surgical shunt or TIPSS. Of these, 334 consecutive patients with cirrhosis who underwent elective surgical shunting (34) or TIPSS (300) for repeated variceal bleeding or refractory ascites were evaluated. Propensity score matching yielded 31 pairs of patients. There were no between-group differences in morbidity and 30-day mortality rates. However, shunt failure was less frequent after surgical shunting than TIPSS (6 of 31 versus 16 of 31; P = 0·016). The 5-year shunt failure-free survival (77 versus 15 per cent; P = 0·008) and overall survival (93 versus 42 per cent; P = 0·037) rates were higher for patients with surgical shunts. Multivariable analysis revealed that a Model for End-Stage Liver Disease (MELD) score exceeding14 and TIPSS were independently associated with shunt failure. In patients with MELD scores of 14 or less, the 5-year overall survival rate remained higher after surgical shunting than TIPSS (100 versus 40 per cent; P < 0·001).

Conclusion

Surgical shunting achieved better results than TIPSS in patients with complicated portal hypertension and low MELD scores.
Comparative pharmacokinetic study of the main components of cortex fraxini after oral administration in normal and hyperuricemic rats
Authors: Wang Yinan , Zhao Min , Ye Hao , Shao Yizhen , Yu Yongbo , Wang Miao , Zhao Chunjie
Published: January 2017

Cortex Fraxini is an important traditional Chinese herbal medicine used for the treatment of gout and hyperuricemia. An efficient and rapid ultra‐performance liquid chromatography mass spectrometry method was developed and validated for simultaneous quantitation of six coumarins (aesculin, fraxin, aesculetin, fraxetin, sopoletin and 7‐hydroxycoumarin) in normal and hyperuricemic rats plasma after oral administration of Cortex Fraxini. The method could successfully be applied for pharmacokinetics studies. The pharmacokinetic behavior of six coumarins in normal and hyperuricemia rats plasma was determined. Results showed that, for some of analytes, the pharmacokinetic parameters (AUC0–t, AUC0–∞, Cmax, Tmax and CL) were significantly different between normal and hyperuricemic rats. The different pharmacokinetic parameters might result from renal impairment or a change of metabolic enzymes in the pathological state. The pharmacokinetic study in pathological state could provide more useful information to guide the clinical use of traditional Chinese herbal medicine.
New Challenges in Family Support: The Use of Digital Technology in Supporting Parents
Authors: Lamberton Lauren , Devaney John , Bunting Lisa
Published: January 2017

This study explores how digital technology is being used to provide innovative family support services (FSS), and the challenges and opportunities that this holds for practitioners in delivering the service. Online services hold the possibility of accessing increasing numbers of parents, and providing support that fits with their own needs and availability. Using the parenting website Netmums as a case study, this article explores how staff who engage with parents online understand their role in both supporting parents and safeguarding children. This exploratory study involved in‐depth semi‐structured online interviews with Netmums′ staff (n = 13). A thematic analysis identified a number of key themes, the most frequently occurring being in relation to: identifying and responding to child safeguarding concerns; and the false impression by parents of anonymity in the online environment. This exploratory research raises more questions than it can answer, especially in relation to managing child safeguarding concerns while maintaining a ‘mum friendly’ approach. Online interventions show promise but there is a need for further evaluation of these forms of intervention. Copyright © 2017 John Wiley & Sons, Ltd.

‘Explores how digital technology is being used to provide innovative family support services’

Key Practitioner Messages

Online FSS provide an alternative, cost‐effective service that can be accessed from anywhere, increasing opportunities for parents to become agents in their own support.

Online FSS meet a much broader and largely unfiltered range of needs compared to offline services but they raise unique challenges in identifying and managing child safeguarding concerns.

In‐depth research into innovative online FSS adds to the wider discussion on the future development of family support.

‘Online FSS provide an alternative, cost‐effective service that can be accessed from anywhere’
Stimulation of neurotrophic factors and inhibition of proinflammatory cytokines by exogenous application of triiodothyronine in the rat model of ischemic stroke
Authors: Sabbaghziarani Fatemeh , Mortezaee Keywan , Akbari Mohammad , Kashani Iraj Ragerdi , Soleimani Mansooreh , Hassanzadeh Gholamreza , Zendedel Adib
Published: January 2017

There is a positive relation between decreases of triiodothyronine (T3) amounts and severity of stroke. The aim of this study was to evaluate the effect of exogenous T3 application on levels of neurogenesis markers in the subventricular zone. Cerebral ischemia was induced by middle cerebral artery occlusion in male Wistar rats. There were 4 experimental groups: sham, ischemic, vehicle, and treatment. Rats were injected with T3 (25 μg/kg, IV injection) at 24 hours after ischemia. Animals were sacrificed at day 7 after ischemia. There were high levels of brain‐derived neurotrophic factor, nestin, and Sox2 expressions in gene and protein levels in the T3 treatment group (P ≤ .05 vs ischemic group). Treatment group showed high levels of sera T3 and thyroxine (T4) but low levels of thyrotropin (TSH), tumor necrosis factor‐α, and interleukin‐6 (P ≤ .05 vs ischemic group) at day 4 after ischemia induction. Findings of this study revealed the effectiveness of exogenous T3 application in the improvement of neurogenesis possibly via regulation of proinflammatory cytokines.
Study of Flow Characteristics of Ultrafine CaCO3 Powders in a Spouted Bed
Authors: Sun Liyan , Wang Shuai , Liu Guodong , Lu Huilin
Published: January 2017

The flow behavior of gas and ultrafine powder in a spouted bed was numerically investigated by using a two‐fluid model coupled with a population balance equation (PBE). The aggregation process is controlled by the PBE, which is solved by the direct quadrature method of moments. The agglomerate diameter is calculated according to the change in particle number. The solid pressure and viscosity were modified for agglomerates on the basis of the kinetic theory of granular flow. Distributions of diameter, solids volume fraction, and velocity are obtained by the new model. The influence of cohesive intensity and gas velocity on the diameter distribution were analyzed. The spout diameter, a vital parameter for the design of spouted beds, was calculated and a calculation formula is proposed.
Stochastic Collision Nanoelectrochemistry: A Review of Recent Developments
Authors: Peng Yue‐Yi , Qian Ruo‐Can , Hafez Mahmoud Elsayed , Long Yi‐Tao
Published: January 2017

Single‐entity electrochemistry mainly focuses on the properties of single nanoscale systems, which provides a new avenue of studying electrochemical processes at the nanoscale rather than in complex ensemble systems. Stochastic collision nanoelectrochemistry (SCNEC), which has emerged as a convenient and fast single‐entity electrochemical analysis method, has gone through significant improvements over the past few years. As a powerful tool for the establishment of multiple analytical strategies, SCNEC has broad applications in electrochemical analysis, catalysis, biosensing, and so forth. This technique is especially promising for the rapid analysis of a single entity with respect to size, concentration, aggregation, and kinetic studies. In this Minireview, we summarize the basic principles and experimental techniques of SCNEC and give a brief overview of the cutting‐edge developments in SCNEC over the past 3 years.
A Bioorganometallic Approach to Study Histidine Kinase Autophosphorylations
Authors: Wang Nan , She Zhe , Ingar Zakiyya , Martic Sanela , Kraatz Heinz‐Bernhard
Published: January 2017

Auto‐phosphorylation of bacterial histidine kinases PhoR, PhoQ, and EnvZ has been investigated using adenosine‐5′‐[γ‐ferrocene] triphosphate (Fc‐ATP) as a cosubstrate for the first time. The study has been carried out in solution and on surface. Results from biochemical multiplex assay and surface electrochemical/optical methods are consistent, which successfully demonstrates that Fc‐ATP is an efficient cosubstrate for histidine kinase auto‐phosphorylations. The study also has discovered that the concentration of Fc‐ATP influences the autophosphorylation efficiency. This developed methodology will provide a powerful tool in studying such biological processes towards further understanding of the involved mechanism.
Mixed‐Linkage Glucan Oligosaccharides Produced by Automated Glycan Assembly Serve as Tools To Determine the Substrate Specificity of Lichenase
Authors: Dallabernardina Pietro , Schuhmacher Frank , Seeberger Peter H. , Pfrengle Fabian
Published: January 2017

The mixed‐linkage (1→3),(1→4)‐d‐glucan (MLG) specific glycosyl hydrolase lichenase is an important biochemical tool for the structural characterization of MLGs. It holds potential for application in the brewery, animal feed, and biofuel industries. Several defined MLG oligosaccharides obtained by automated glycan assembly are used to analyze the substrate specificities of Bacillus subtilis lichenase. Two glucose building blocks (BBs), equipped with a temporary fluorenylmethyloxycarbonyl chloride (Fmoc) protecting group in the C‐3 or C‐4 position, served to assemble different oligosaccharides by using an automated oligosaccharide synthesizer. Light‐induced cleavage of the glycan products from the solid support followed by global deprotection provided seven MLG oligosaccharides of different length and connectivity. After incubation of the MLG oligosaccharides with lichenase, the digestion products were analyzed by HPLC‐MS. These digestion experiments provided insights into the enzyme's active site that is in line with other recent evidence suggesting that the substrate specificity of lichenases has to be reconsidered. These results demonstrate that synthetic MLG oligosaccharides are useful tools to analyze mixed‐linkage β‐glucanases.
Direct and Autocatalytic Reductive Elimination from Gold Complexes ([(Ph3P)Au(Ar)(CF3)(X)], X=F, Cl, Br, I): The Key Role of Halide Ligands
Authors: Bhattacharjee Rameswar , Nijamudheen A. , Datta Ayan
Published: January 2017

Kinetic and thermodynamic preferences for the reductive elimination of Caryl−CF3, Caryl−X, Caryl−P, and CF3−X bonds and competitive phosphine dissociation from a series of AuIII complexes [(Ph3P)Au(Ar)(CF3)(X)] (1 X; Ar=4‐Me−C6H4; X=F, Cl, Br, I) are studied computationally. Kinetically, the most favorable pathways were found to consist of an initial phosphine dissociation from complex 1 X, which furnished the respective three‐coordinate AuIII complexes [Au(Ar)(CF3)(X)] (2 X). The computed enthalpy barriers for various reductive elimination reactions from complex 2 X by a direct (or uncatalyzed) mechanism showed that Caryl−CF3 bond formation was the most favorable fate for any X group. When the direct elimination was compared with an autocatalytic mechanism that proceeded through the formation of a mixed‐valent binuclear AuIII−AuI intermediate, the preference for the formation of a Caryl−CF3 bond is dependent on the nature of the bridging halide atom and follows the order F>Cl>Br>I. Concomitantly, the selectivity for the formation of Caryl−X bonds for various X atoms follows the opposite trend. The preference for the direct and autocatalytic processes is controlled entirely by the nature of the halide ligand. The predicted mechanisms and product selectivity trends for various halides show excellent agreement with recent experimental observation. The selectivity of various reductive elimination pathways was rationalized by using molecular orbital theory and distortion–interaction model analyses. Attractive interactions between the AuI complex and complex 2X were found to reduce the activation barrier for Caryl−X elimination and critically control the selectivity of the product formation.
Effect of a solvent‐free acetylation treatment on reinforcements permeability and tensile behaviour of flax/epoxy and flax/wood fibre/epoxy composites
Authors: El Boustani Meriem , Lebrun Gilbert , Brouillette François , Belfkira Ahmed
Published: January 2017

Acetylation is a common way to enhance interfacial adhesion between natural fibres and polymeric matrices in composites. This work investigates the effect of a solvent‐free environmentally friendly acetylation treatment of short flax and kraft fibres on the impregnation behaviour and tensile properties of flax fibre/epoxy composites. Untreated and acetylated fibres have been used to prepare fibre mats, which were next studied for their morphology, their permeability to liquid epoxy, and their ability to adhere to the epoxy matrix after cure. The results show that acetylation enhances the roughness of flax fibres and improves fibre‐matrix interaction, but reduces the permeability of the fibre mats and the intrinsic properties of fibres, thus leading to slightly lower composite modulus and strength. The proposed treatment is an interesting option to improve the affinity between natural fibres and polymeric matrices, but more work will be required to improve the interfacial adhesion without damaging the fibres.
The novel fusion transcript NR5A2‐KLHL29FT is generated by an insertion at the KLHL29 locus
Authors: Sun Zhenguo , Ke Xiquan , Salzberg Steven L. , Kim Daehwan , Antonescu Valentin , Cheng Yulan , Huang Binbin , Song Jee Hoon , Abraham John M. , Ibrahim Sariat , Tian Hui , Meltzer Stephen J.
Published: January 2017

BACKGROUND

Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers.

METHODS

RNA sequencing (RNA‐Seq) and TopHat‐Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)‐Kelch‐like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement. Next, the expression of NR5A2‐KLHL29FT was measured by quantitative real‐time polymerase chain reaction in colon cancers and matched corresponding normal epithelia.

RESULTS

The authors identified the FT NR5A2‐KLHL29FT in normal and cancerous epithelia. While investigating this transcript, it was unexpectedly found that it was due to an uncharacterized polymorphic germline insertion of the NR5A2 sequence from chromosome 1 into the KLHL29 locus at chromosome 2, rather than a chromosomal rearrangement. This germline insertion, which occurred at a population frequency of 0.40, appeared to bear no relationship to cancer development. Moreover, expression of NR5A2‐KLHL29FT was validated in RNA specimens from samples with insertions of NR5A2 at the KLHL29 gene locus, but not from samples without this insertion. It is interesting to note that NR5A2‐KLH29FT expression levels were significantly lower in colon cancers than in matched normal colonic epithelia (P =.029), suggesting the potential participation of NR5A2‐KLHL29FT in the origin or progression of this tumor type.

CONCLUSIONS

NR5A2‐KLHL29FT was generated from a polymorphism insertion of the NR5A2 sequence into the KLHL29 locus. NR5A2‐KLHL29FT may influence the origin or progression of colon cancer. Moreover, researchers should be aware that similar FTs may occur due to transchromosomal insertions that are not correctly annotated in genome databases, especially with current assembly algorithms. Cancer 2017;123:1507–1515. © 2017 American Cancer Society.
Measurement of T‐Cell Telomere Length Using Amplified‐Signal FISH Staining and Flow Cytometry
Authors: Henning Andrea L. , Levitt Danielle E. , Vingren Jakob L. , McFarlin Brian K.
Published: January 2017

Exposure to pathogen‐associated molecular patterns (PAMPS), damage‐associated molecular patterns (DAMPS), and physiologically challenging stimuli either positively or negatively affect leukocyte maturity. Cellular maturity has implications for the effectiveness of host response to bacterial or viral infection and/or tissue injury. Thus, the ability to accurately assess cellular maturity and health is important to fully understand immune status and function. The most common technique for measuring cellular maturity is to measure telomere length; however, existing techniques are not optimized for single‐cell measurements using flow cytometry. Specifically, existing methods used to measure telomere length are PCR‐based, making it difficult for a researcher to measure maturity within specific leukocyte subsets (e.g., T cells). In this report, we describe a new approach for the measurement of telomere length within individual T cells using an amplified fluorescence in situ hybridization (FISH) technique (PrimeFlow RNA Assay). The unique aspect of this technique is that it amplifies the fluorescent signal rather than the target up to 3000‐fold, resulting in the detection of as few as 1 copy of the target nucleic acid. While the current technique focuses on human T cells, this method can be broadly applied to a variety of cell types and disease models. © 2017 by John Wiley & Sons, Inc.
Identification of Human Memory‐Like NK Cells
Authors: Kovalenko Elena I. , Streltsova Maria A. , Kanevskiy Leonid M. , Erokhina Sophia A. , Telford William G.
Published: January 2017

Our understanding of NK biology is increased dramatically, a product of improved flow‐cytometric techniques for analyzing these cells. NK cells undergo significant changes in repertoire during differentiation. A repeating stimulus, such as a cytomegalovirus infection, may result in accumulation of certain types of highly differentiated NK cells designated as memory‐like, or adaptive NK cells. Adaptive NK cells are capable of rapid expansion and effective response to the recall stimulus. These cells differ significantly from conventional NK cells both functionally and phenotypically. Here we describe an approach for identification and analysis of adaptive NK cells in human peripheral blood. CD57‐positive cells with high expression of activating‐receptor NKG2C, increased expression of KIR receptors, lack of co‐expression with inhibitory receptor NKG2A, and decreased expression of activating receptor NCR3 (NKp30) all characterize this cell type. The flow‐cytometric method described below can identify this NK cell subset on a relatively simple flow cytometer. © 2017 by John Wiley & Sons, Inc.
Standardization, Calibration, and Control in Flow Cytometry
Authors: Wang Lili , Hoffman Robert A.
Published: January 2017

Because flow cytometers are designed to measure particle characteristics, particles are the most common materials used to calibrate, control, and standardize the instruments. Definitions and cautions are provided for common terms to alert the reader to critical distinctions in meaning. This unit presents extensive background on particle types and cautions and describes practical aspects of methods to standardize and calibrate instruments. Procedures are provided to characterize performance in terms of optical alignment, fluorescence and light scatter resolution, and sensitivity. Finally, suggestions follow for analyzing particles used for calibration. © 2017 by John Wiley & Sons, Inc.
Human Induced Pluripotent Stem (hiPS) Cells from Urine Samples: A Non‐Integrative and Feeder‐Free Reprogramming Strategy
Authors: Steichen Clara , Si‐Tayeb Karim , Wulkan Fanny , Crestani Thayane , Rosas Graça , Dariolli Rafael , Pereira Alexandre C. , Krieger Jose E.
Published: January 2017

Human induced pluripotent stem (hiPS) cell technology has already revolutionized some aspects of fundamental and applied research such as study of disease mechanisms and pharmacology screening. The first clinical trial using hiPS cell‐derived cells began in Japan, only 10 years after the publication of the proof‐of concept article. In this exciting context, strategies to generate hiPS cells have evolved quickly, tending towards non‐invasive protocols to sample somatic cells combined with “safer” reprogramming strategies. In this unit, we describe a protocol combining both of these advantages to generate hiPS cells with episomal plasmid transfection from urine samples of individuals carrying the desired genotype. Based on previous published works, this simplified protocol requires minimal equipment and reagents, and is suitable both for scientists familiar with the hiPS cells technology and neophytes. HiPS cells displaying classical features of pluripotency and suitable for all desired downstream applications are generated rapidly (<10 weeks) and with high efficiency. © 2017 by John Wiley & Sons, Inc.
Generating Exome Enriched Sequencing Libraries from Formalin‐Fixed, Paraffin‐Embedded Tissue DNA for Next‐Generation Sequencing
Authors: Marosy Beth A. , Craig Brian D. , Hetrick Kurt N. , Witmer P. Dane , Ling Hua , Griffith Sean M. , Myers Benjamin , Ostrander Elaine A. , Stanford Janet L. , Brody Lawrence C. , Doheny Kimberly F.
Published: January 2017

This unit describes a technique for generating exome‐enriched sequencing libraries using DNA extracted from formalin‐fixed paraffin‐embedded (FFPE) samples. Utilizing commercially available kits, we present a low‐input FFPE workflow starting with 50 ng of DNA. This procedure includes a repair step to address damage caused by FFPE preservation that improves sequence quality. Subsequently, libraries undergo an in‐solution‐targeted selection for exons, followed by sequencing using the Illumina next‐generation short‐read sequencing platform. © 2017 by John Wiley & Sons, Inc.
Diagnosis of Spinocerebellar Ataxias Caused by Trinucleotide Repeat Expansions
Authors: Martindale Joanne E.
Published: January 2017

Spinocerebellar ataxias (SCAs) are a group of disorders that are both clinically and genetically heterogeneous. They usually demonstrate onset in adulthood, but some forms may have juvenile or infantile onset. There are many different types of SCA, demonstrating different modes of inheritance and types of mutation. The most common forms are due to dominantly inherited expansions in trinucleotide repeat sequences located within the coding region of the relevant genes, and these are readily identifiable by molecular genetic testing. In general, it is possible to test for these disorders using PCR‐based assays, amplifying across the trinucleotide repeat regions and sizing the PCR products to determine the number of repeats. Larger expansions are generally associated with a more severe presentation of the disorder, and alternative methods may be necessary to detect these alleles. This protocol describes methods for detecting normal and expanded triplet repeat alleles in the most common SCA genes. © 2017 by John Wiley & Sons, Inc.
Highly Expandable Human iPS Cell–Derived Neural Progenitor Cells (NPC) and Neurons for Central Nervous System Disease Modeling and High‐Throughput Screening
Authors: Cheng Chialin , Fass Daniel M. , Folz‐Donahue Kat , MacDonald Marcy E. , Haggarty Stephen J.
Published: January 2017

Reprogramming of human somatic cells into induced pluripotent stem (iPS) cells has greatly expanded the set of research tools available to investigate the molecular and cellular mechanisms underlying central nervous system (CNS) disorders. Realizing the promise of iPS cell technology for the identification of novel therapeutic targets and for high‐throughput drug screening requires implementation of methods for the large‐scale production of defined CNS cell types. Here we describe a protocol for generating stable, highly expandable, iPS cell–derived CNS neural progenitor cells (NPC) using multi‐dimensional fluorescence activated cell sorting (FACS) to purify NPC defined by cell surface markers. In addition, we describe a rapid, efficient, and reproducible method for generating excitatory cortical‐like neurons from these NPC through inducible expression of the pro‐neural transcription factor Neurogenin 2 (iNgn2‐NPC). Finally, we describe methodology for the use of iNgn2‐NPC for probing human neuroplasticity and mechanisms underlying CNS disorders using high‐content, single‐cell‐level automated microscopy assays. © 2017 by John Wiley & Sons, Inc.
Next‐Generation Sequencing for Identification of EMS‐Induced Mutations in Caenorhabditis elegans
Authors: Lehrbach Nicolas J. , Ji Fei , Sadreyev Ruslan
Published: January 2017

Forward genetic analysis using chemical mutagenesis in model organisms is a powerful tool for investigation of molecular mechanisms in biological systems. In the nematode, Caenorhabditis elegans, mutagenesis screens using ethyl methanesulfonate (EMS) have led to important insights into genetic control of animal development and physiology. A major bottleneck to this approach is identification of the causative mutation underlying a phenotype of interest. In the past, this has required time‐consuming genetic mapping experiments. More recently, next‐generation sequencing technologies have allowed development of new methods for rapid mapping and identification of EMS‐induced lesions. In this unit we describe a protocol to map and identify EMS‐induced mutations in C. elegans. © 2017 by John Wiley & Sons, Inc.
Visualizing Changes in Neuronal Dendritic Morphology in Response to Stress and Pharmacological Challenge
Authors: Wellman Cara L.
Published: January 2017

This unit outlines a protocol for Golgi staining, which has been used extensively to reliably and quantitatively assess alterations in dendritic arborization and spine density as a result of a variety of factors, including chronic administration of glucocorticoids, chronic stress, and pharmacological manipulations. The method stains neurons in their entirety, allowing for sophisticated analyses of branch lengths and numbers as well as patterns of dendritic branching. Advantages of the technique include its usefulness in multisite collaborations and its utility in visualizing neurons in multiple regions within the same brain. Given that it typically labels approximately one in one hundred neurons, many neurons per region of interest can be sampled per animal, greatly increasing the ability to obtain a representative sample of neurons. Limitations include its time‐consuming nature, the hazardous chemicals employed, and the inability to use the stain to identify discrete subpopulations of neurons based on their projections, activation, or protein expression. © 2017 by John Wiley & Sons, Inc.
Growth of crystalline semiconductor structures on amorphous substrates for photovoltaic applications
Authors: Boeck T. , Ringleb F. , Bansen R.
Published: January 2017

The growth of defined crystalline structures on amorphous materials is an almost generally difficult task. Due to the lack of a crystallographic lattice, no epitaxial intergrowth can be realized. However, for many applications the growth of crystalline layers or microstructures on such substrates, or on amorphous or nanocrystalline intermediate layers is required. For large area applications such as solar cells, glass is a particularly favored material. The article presents two studies from the field of photovoltaics. Both are characterized by a locally selective seeding: the growth of crystalline Si on glass by steady‐state solution growth on a partially crystallized Si seed layer, and the preparation of CuInSe2 absorber islands for micro concentrator solar cells from spatially confined metallic indium droplets.
The most primitive metazoan animals, the placozoans, show high sensitivity to increasing ocean temperatures and acidities
Authors: Schleicherová Dáša , Dulias Katharina , Osigus Hans‐Jűrgen , Paknia Omid , Hadrys Heike , Schierwater Bernd
Published: January 2017

The increase in atmospheric carbon dioxide (CO2) leads to rising temperatures and acidification in the oceans, which directly or indirectly affects all marine organisms, from bacteria to animals. We here ask whether the simplest—and possibly also the oldest—metazoan animals, the placozoans, are particularly sensitive to ocean warming and acidification. Placozoans are found in all warm and temperate oceans and are soft‐bodied, microscopic invertebrates lacking any calcified structures, organs, or symmetry. We here show that placozoans respond highly sensitive to temperature and acidity stress. The data reveal differential responses in different placozoan lineages and encourage efforts to develop placozoans as a potential biomarker system.
Effects of predation risk on behavior, hormone levels, and reproductive success of plateau pikas
Authors: Yin Baofa , Yang Shengmei , Shang Guozhen , Wei Wanhong
Published: January 2017

Predation is a strong selective force that affects animal population dynamics either through direct killing or predation risk effects. Although recent empirical research has shown that the non‐consumptive effect of predator risk on prey dynamics can be as large (or even larger) as direct effects, little is known about the strength of predation risk effects in wild populations or the physiological mechanisms that mediate them. Here, we test both the predator‐sensitive food hypothesis and predation‐stress hypothesis in a single system by investigating activity budgets, stress/sex hormone levels, and demography of plateau pikas (Ochotona curzoniae) and their predators in Haibei Alpine Meadow Ecosystem Research Station of the Chinese Academy of Science. During the study period (2009 and 2010), plateau pikas experienced various predation pressures due to many predators being poisoned in 2010. In the year of high predator numbers, pikas spent more time on vigilant duty and less time foraging and they also showed higher plasma corticosterone levels and lower plasma estradiol and testosterone levels. Reproductive success and male with developed testes also reduced in the year of higher predation risk. In general, our results support both the predator‐sensitive food and predation‐stress hypothesis. Predator‐induced risk affects prey reproduction by changes in feeding patterns and stress physiology.
Distinct genecological patterns in seedlings ofNorway spruce and silver fir from a mountainous landscape
Authors: Frank Aline , Sperisen Christoph , Howe Glenn Thomas , Brang Peter , Walthert Lorenz , St.Clair John Bradley , Heiri Caroline
Published: January 2017

Understanding the genecology of forest trees is critical for gene conservation, for predicting the effects of climate change and climate change adaptation, and for successful reforestation. Although common genecological patterns have emerged, species‐specific details are also important. Which species are most vulnerable to climate change? Which are the most important adaptive traits and environmental drivers of natural selection? Even though species have been classified as adaptive specialists vs. adaptive generalists, large‐scale studies comparing different species in the same experiment are rare. We studied the genecology of Norway spruce (Picea abies) and silver fir (Abies alba), two co‐occurring but ecologically distinct European conifers in Central Europe. For each species, we collected seed from more than 90 populations across Switzerland, established a seedling common‐garden test, and developed genecological models that associate population variation in seedling growth and phenology to climate, soil properties, and site water balance. Population differentiation and associations between seedling traits and environmental variables were much stronger for Norway spruce than for silver fir, and stronger for seedling height growth than for bud phenology. In Norway spruce, height growth and second flushing were strongly associated with temperature and elevation, with seedlings from the lowlands being taller and more prone to second flush than seedlings from the Alps. In silver fir, height growth was more weakly associated with temperature and elevation, but also associated with water availability. Soil characteristics explained little population variation in both species. We conclude that Norway spruce has become an adaptive specialist because trade‐offs between rapid juvenile growth and frost avoidance have subjected it to strong diversifying natural selection based on temperature. In contrast, because silver fir has a more conservative growth habit, it has evolved to become an adaptive generalist. This study demonstrates that co‐occurring tree species can develop very different adaptive strategies under identical environmental conditions, and suggests that Norway spruce might be more vulnerable to future maladaptation due to rapid climate change than silver fir.
Infectious hematopoietic necrosis virus virological and genetic surveillance 2000–2012
Authors: Breyta Rachel , Brito Ilana , Kurath Gael , LaDeau Shannon
Published: January 2017

Surveillance records of the acute RNA pathogen of Pacific salmonid fish infectious hematopoietic necrosis virus are combined for the first time to enable landscape‐level ecological analyses and modeling. The study area is the freshwater ecosystems of the large Columbia River watershed in the U.S. states of Washington, Oregon, and Idaho, as well as coastal rivers in Washington and Oregon. The study period is 2000–2012, and records were contributed by all five resource management agencies that operate conservation hatcheries in the study area. Additional records from wild fish were collected from the National Wild Fish Health Survey, operated by the U.S. Fish and Wildlife Survey. After curation and normalization, the data set consists of 6766 records, representing 1146 sample sites and 15 different fish hosts. The virus was found in an average of 12.4% of records, and of these 66.2% also have viral genetic analysis available. This data set is used to conduct univariate ecological and epidemiological analyses and develop a novel hierarchical landscape transmission model for an aquatic pathogen.
Herbivory enhances the diversity of primary producers in pond ecosystems
Authors: Leibold Mathew A. , Hall Spencer R. , Smith Val H. , Lytle David A.
Published: January 2017

Diversity of primary producer is often surprisingly high, despite few limiting factors such as nutrients and light to facilitate species coexistence. In theory, the presence of herbivores could increase the diversity of primary producers, resolving this “paradox of the plankton.” Little experimental evidence supports this natural enemies hypothesis, but previous tests suffer from several deficiencies. Previous experiments often did not allow for multigeneration effects; utilized low diversity assemblages of herbivores; and limited opportunities for new primary producer and herbivore species to colonize and undergo species sorting that favors some species over others. Using pond plankton, we designed a mesocosm experiment that overcame these problems by allowing more time for interactions over multiple generations, openness to allow new colonists, and manipulated higher diversity of primary producers and grazers than have previous studies. With this design, the presence of zooplankton grazers doubled phytoplankton richness. The additional phytoplankton species in grazed mesocosms were larger, and therefore likely more grazer resistant. Furthermore, phytoplankton richness in grazed mesocosms was similar to that observed in natural ponds whereas it was much lower in mesocosms without grazers. However, stoichiometric imbalance caused by variation in nitrogen : phosphorus ratios and light supply did not alter phytoplankton richness. Therefore, grazers enhanced primary producer richness more strongly than ratios of nutrient supply (even though both grazing and ratios of resource supply altered composition of primary producer assemblages). Taken together, these experimental and field data show that grazing from a diverse assemblage of herbivores greatly elevated richness of phytoplankton producers in pond ecosystems.
Unified Theory of Electromagnetic Induction and Magnetic Resonant Coupling
Authors: IMURA TAKEHIRO , HORI YOICHI
Published: January 2017

The difference between electromagnetic induction and magnetic resonant coupling was pointed out in the first proposal of electromagnetic resonant coupling. However, there was no clear technical comparison between the two methods. Therefore, in this study, five circuits are compared by using a phasor diagram, which is a basic and well‐known method in electric circuit theory. The transition from typical electromagnetic induction to magnetic resonant coupling is shown. The mechanism of the high efficiency and high‐power transfer across a large air gap and displacement is discussed, where the primary‐ and secondary‐side resonant frequencies are the same. From the above discussion, we conclude that when the specific conditions of electromagnetic induction are satisfied, the wireless power transfer can be categorized as electromagnetic resonant coupling. The unified theory of electromagnetic induction and magnetic resonant coupling is verified through experiment.
System Voltage Control Based on Potential Game Theory Considering PV Output Prediction Error
Authors: ANDO SHO , GOMI TOMOYUKI , IWAMOTO SHINICHI
Published: January 2017

Recently, in Japan, large‐scale introduction of photovoltaics (PVs) has been under way. This development increases the likelihood of system voltage increase and fluctuations, which can be prevented by employing PV output prediction. In this study, we focus our attention on applying PV output prediction to system operation with the objective of system voltage control. In this paper, 30‐min ahead prediction is assumed according to prior research with prediction error consideration. System voltages of 30 min ahead are estimated and are controlled in advance by using transformer taps and static capacitors. In this paper, voltage control is proposed for coordinating control, which is based on one of the games in the game theory, potential game. The validity of the proposed method is confirmed by running simulations using a modified IEEE 30 bus system. By applying the proposed method, both the voltage deviations and control counts improved considerably compared to a conventional method.
Type 1 diabetes pathogenesis is modulated by spontaneous autoimmune responses to endogenous retrovirus antigens in NOD mice
Authors: Bashratyan Roman , Regn Danielle , Rahman M. Jubayer , Marquardt Kristi , Fink Elizabeth , Hu Wen‐Yuan , Elder John H. , Binley James , Sherman Linda A. , Dai Yang D.
Published: January 2017

Secreted microvesicles (MVs) are potent inflammatory triggers that stimulate autoreactive B and T cells, causing Type 1 Diabetes in non‐obese diabetic (NOD) mice. Proteomic analysis of purified MVs released from islet cells detected the presence of endogenous retrovirus (ERV) antigens, including Env and Gag sequences similar to the well‐characterized murine leukemia retroviruses. This raises the possibility that ERV antigens may be expressed in the pancreatic islets via MV secretion. Using virus‐like particles produced by co‐expressing ERV Env and Gag antigens, and a recombinant gp70 Env protein, we demonstrated that NOD but not diabetes‐resistant mice developed anti‐Env autoantibodies that increase in titer as disease progresses. A lentiviral‐based RNA interference knockdown of Gag revealed that Gag contributes to the MV‐induced T‐cell response, whose diabetogenic function can be demonstrated via cell‐transfer into immune‐deficient mice. Finally, we observed that Gag and Env are expressed in NOD islet‐derived primary mesenchymal stem cells (MSCs). However, MSCs derived from the islets of diabetes‐resistant mice do not express the antigens. Taken together, abnormal ERV activation and secretion of MVs may induce anti‐retroviral responses to trigger autoimmunity.
Functional and structural characterization of four mouse monoclonal antibodies to complement C3 with potential therapeutic and diagnostic applications
Authors: Subías Hidalgo Marta , Yébenes Hugo , Rodríguez‐Gallego César , Martín‐Ambrosio Adrián , Domínguez Mercedes , Tortajada Agustin , Rodríguez de Córdoba Santiago , Llorca Oscar
Published: January 2017

C3 is the central component of the complement system. Upon activation, C3 sequentially generates various proteolytic fragments, C3a, C3b, iC3b, C3dg, each of them exposing novel surfaces, which are sites of interaction with other proteins. C3 and its fragments are therapeutic targets and markers of complement activation. We report the structural and functional characterization of four monoclonal antibodies (mAbs) generated by immunizing C3‐deficient mice with a mixture of human C3b, iC3b and C3dg fragments, and discuss their potential applications. This collection includes three mAbs interacting with native C3 and inhibiting AP complement activation; two of them by blocking the cleavage of C3 by the AP C3‐converase and one by impeding formation of the AP C3‐convertase. The interaction sites of these mAbs in the target molecules were determined by resolving the structures of Fab fragments bound to C3b and/or iC3b using electron microscopy. A fourth mAb specifically recognizes the iC3b, C3dg, and C3d fragments. It binds to an evolutionary‐conserved neoepitope generated after C3b cleavage by FI, detecting iC3b/C3dg deposition over opsonized surfaces by flow cytometry and immunohistochemistry in human and other species. Because well‐characterized anti‐complement mAbs are uncommon, the mAbs reported here may offer interesting therapeutic and diagnostic opportunities.
Ostracism, resources, and the perception of human motion
Authors: Gorman Jamie L. , Harber Kent D. , Shiffrar Maggie , Quigley Karen S.
Published: January 2017

Is perception of human motion affected by psychosocial resources? According to the Resources and Perception Model, perception is jointly affected by subjective threat and psychosocial resources that buffer threat. Two experiments tested whether social threat (i.e., ostracism) and psychosocial resources affect perception of human motion. Observers attempted to identify human movement in ambiguous point‐light displays after being ostracized or not ostracized. Additionally, trait resources (self‐esteem plus social support) were measured (Studies 1 and 2), and self‐affirmation was manipulated (Study 2). Study 1 showed that ostracism reduced sensitivity for detecting human motion but not among people with ample trait resources. Study 2 replicated this ostracism‐by‐trait resources interaction. It also showed that self‐affirmation improved human motion perception for all included participants but only benefited ostracized participants with ample trait resources. These studies show that a basic visual skill—detecting human motion—is jointly affected by social threats and psychosocial resources.