bluuebunny/crossref_metadata_2025 huggingface dataset:
C. elegansdiscriminate colors without eyes or opsins
Authors: Ghosh D. Dipon , Jin Xin , Nitabach Michael
Published: December 2016

Here we establish that, contrary to expectations,Caenorhabditis elegansnematode worms possess a color discrimination system despite lacking any opsin or other known visible light photoreceptor genes. We found that white light guidesC. elegansforaging decisions away from harmful bacteria that secrete a blue pigment toxin. Absorption of amber light by this blue pigment toxin alters the color of light sensed by the worm, and thereby triggers an increase in avoidance. By combining narrow-band blue and amber light sources, we demonstrated that detection of the specific blue:amber ratio by the worm guides its foraging decision. These behavioral and psychophysical studies thus establish the existence of a color detection system that is distinct from those of other animals.
What rhythmic perception and amusia can tell us about vocal social communication in schizophrenia
Authors: Mitchell Rachel L. C. , Gamez Krystal , Bolgar Joshua , Neustadter Eli S. , Calkins Monica E. , Moore Tyler M. , Leitman David I.
Published: December 2016

Background

Perceiving social intent throughvocal intonation is impaired in schizophrenia; thisdysprosodia partly arisingfrom impaired pitch perception.Individuals with amusia (tone-deafness) are insensitive to pitch change andalso demonstrate prosody deficits. Sensitivity to rhythm is reduced in amusia when tonal sequences contain pitch changes (polytonic), but is normal for monotonic sequences, suggesting perceptual impairment originates at a secondary processing stage where pitch- and time-relatedcues are yoked. Here, we sought to ascertain: 1) whether schizophreniapatients demonstrate rhythmic deficits, 2) whether suchdeficits are restricted to polytonic sequences, and 3) how pitch and rhythm perception relate to prosodic processing.

Methods

Seventy-sixparticipants (33 schizophrenia) completed tasks assessing pitch and prosody perception, as well as monotonic and polytonic rhythmic perception.

Results

Increasing tone-deafness correlated with pitch-dependent rhythm detection impairments. Pitch and prosody correlated across all participants. Schizophreniapatients displayed basic time and pitch deficits. Correlations and path analyses indicated prosodic processing is an associatedfunction of pitch and pitch-dependent rhythm perception,with pure temporal processing playing an indirect role.In schizophrenia, deficits in monotonic and polytonic rhythmic perception did not contribute to prosodic processing dysfunction, and montonic rhythmic dysfunction and pitch perception did not covary.

Conclusions

Exploring similarities between amusia and schizophrenia focused our characterization of prosodic processing as the function of sub-processes reflecting pitch and time perception,whichare prerequisite for prosodic processing. The uniqueness of dysprosodia in schizophrenia relative to other illnesses may be measured by idiosyncrasy in the pattern and magnitude of the sub-process task relationships.
Neural Homophily: Similar Neural Responses Predict Friendship
Authors: Parkinson Carolyn M. , Kleinbaum Adam M. , Wheatley Thalia
Published: December 2016

We resemble our friends on a wide range of dimensions (e.g., age, gender), but do similarities between friends reflect deeper similarities in how we perceive, interpret, and respond to the world? To find out, we characterized the social network of a cohort of 279 students, a subset of whom participated in a functional magnetic resonance imaging (fMRI) study involving free-viewing of video stimuli. We compared fMRI response time series between corresponding brain regions across pairs of individuals and found that neural response similarity decreased with increasing distance in the social network. These effects persisted after controlling for demographic similarity. Further, it was possible to accurately classify the distance between individuals in their social network based on the similarity of their fMRI response time series across brain regions. These results suggest that we are exceptionally similar to our friends in how we perceive and react to the world around us.
Pan-Cancer Analysis Reveals Technical Artifacts in TCGA Germline Variant Calls
Authors: Buckley Alexandra R. , Standish Kristopher A. , Bhutani Kunal , Ideker Trey , Carter Hannah , Harismendy Olivier , Schork Nicholas J.
Published: December 2016

The degree to which germline variation drives cancer development and shapes tumor phenotypes remains largely unexplored, possibly due to a lack of large scale publicly available germline data for a cancer cohort. Here we called germline variants on 9,618 cases from The Cancer Genome Atlas (TCGA) database representing 31 cancer types. We identified batch effects affecting loss of function (LOF) variant calls that can be traced back to differences in the way the sequence data were generated both within and across cancer types. Overall, LOF indel calls were more sensitive to technical artifacts than LOF Single Nucleotide Variant (SNV) calls. In particular, whole genome amplification of DNA prior to sequencing led to an artificially increased burden of LOF indel calls, which confounded association analyses relating germline variants to tumor type despite stringent indel filtering strategies. Due to the inherent noise we chose to remove all 614 amplified DNA samples, including all acute myeloid leukemia and virtually all ovarian cancer samples, from the final dataset. This study demonstrates how insufficient quality control can lead to false positive germlinetumor type associations and draws attention to the need to be sensitive to problems associated with a lack of uniformity in data generation in TCGA data.

Author Summary

Cancer research to date has largely focused on genetic aberrations specific to tumor tissue. In contrast, the degree to which germline, or inherited, variation contributes to tumorigenesis remains unclear, possibly due to a lack of accessible germline variant data. In this study we identify germline variants in 9,618 samples using raw germline exome data from The Cancer Genome Atlas (TCGA). There are substantial differences in the way exome sequence data was generated both across and within cancer types in TCGA. We observe that differences in sequence data generation introduced batch effects, or variation that is due to technical factors not true biological variation, in our variant data. Most notably, we observe that amplification of DNA prior to sequencing resulted in an excess of predicted damaging indel variants. We show how these batch effects can confound germline association analyses if not properly addressed. Our study highlights the difficulties of working with large public genomic datasets like TCGA where samples are collected over time and across data centers, and particularly cautions the use of amplified DNA samples for genetic association analyses.
Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software
Authors: Gardner Paul P. , Paterson James M. , McGimpsey Stephanie , Ashari-Ghomi Fatemeh , Umu Sinan U. , Pawlik Aleksandra , Gavryushkin Alex , Black Michael A.
Published: December 2016

Background

Computational biology provides widely used and powerful software tools for testing and making inferences about biological data. In the face of rapidly increasing volumes of data, heuristic methods that trade software speed for accuracy may be employed. We are have studied these trade-offs using the results of a large number of independent software benchmarks, and evaluated whether external factors are indicative of accurate software.

Method

We have extracted accuracy and speed ranks from independent benchmarks of different bioinformatic software tools, and evaluated whether the speed, author reputation, journal impact, recency and developer efforts are indicative of accuracy.

Results

We found that software speed, author reputation, journal impact, number of citations and age are all unreliable predictors of software accuracy. This is unfortunate because citations, author and journal reputation are frequently cited reasons for selecting software tools. However, GitHub-derived records and high version numbers show that the accurate bioinformatic software tools are generally the product of many improvements over time, often from multiple developers.

Discussion

We also find that the field of bioinformatics has a large excess of slow and inaccurate software tools, and this is consistent across many sub-disciplines. Meanwhile, there are few tools that are middle-of-road in terms of accuracy and speed trade-offs. We hypothesise that a form of publication-bias influences the publication and development of bioinformatic software. In other words, software that is intermediate in terms of both speed and accuracy may be difficult to publish - possibly due to author, editor and reviewer practices. This leaves an unfortunate hole in the literature as the ideal tools may fall into this gap. For example, high accuracy tools are not always useful if years of CPU time are required, while high speed is not useful if the results are also inaccurate.
Decoding visual stimuli in human brain by using Anatomical Pattern Analysis on fMRI images
Authors: Yousefnezhad Muhammad , Zhang Daoqiang
Published: December 2016

A universal unanswered question in neuroscience and machine learning is whether computers can decode the patterns of the human brain. Multi-Voxels Pattern Analysis (MVPA) is a critical tool for addressing this question. However, there are two challenges in the previous MVPA methods, which include decreasing sparsity and noises in the extracted features and increasing the performance of prediction. In overcoming mentioned challenges, this paper proposes Anatomical Pattern Analysis (APA) for decoding visual stimuli in the human brain. This framework develops a novel anatomical feature extraction method and a new imbalance AdaBoost algorithm for binary classification. Further, it utilizes an Error-Correcting Output Codes (ECOC) method for multi-class prediction. APA can automatically detect active regions for each category of the visual stimuli. Moreover, it enables us to combine homogeneous datasets for applying advanced classification. Experimental studies on 4 visual categories (words, consonants, objects and scrambled photos) demonstrate that the proposed approach achieves superior performance to state-of-the-art methods.
Mapping Autosomal Recessive Intellectual Disability: Combined Microarray and Exome Sequencing Identifies 26 Novel Candidate Genes in 192 Consanguineous Families
Authors: Harripaul Ricardo , Vasli Nasim , Mikhailov Anna , Rafiq Muhammad Arshad , Mittal Kirti , Windpassinger Christian , Sheikh Taimoor I. , Noor Abdul , Mahmood Huda , Downey Samantha , Johnson Maneesha , Vleuten Kayla , Bell Lauren , Ilyas Muhammad , Khan Falak Sher , Khan Valeed , Moradi Mohammad , Ayaz Muhammad , Naeem Farooq , Heidari Abolfazl , Ahmed Iltaf , Ghadami Shirin , Agha Zehra , Zeinali Sirous , Qamar Raheel , Mozhdehipanah Hossein , John Peter , Mir Asif , Ansar Muhammad , French Leon , Ayub Muhammad , Vincent John B.
Published: December 2016

Approximately 1% of the global population is affected by intellectual disability (ID), and the majority receive no molecular diagnosis. Previous studies have indicated high levels of genetic heterogeneity, with estimates of more than 2500 autosomal ID genes, the majority of which are autosomal recessive (AR). Here, we combined microarray genotyping, homozygosity-by-descent (HBD) mapping, copy number variation (CNV) analysis, and whole exome sequencing (WES) to identify disease genes/mutations in 192 multiplex Pakistani and Iranian consanguineous families with non-syndromic ID. We identified definite or candidate mutations (or CNVs) in 51% of families in 72 different genes, including 26 not previously reported for ARID. The new ARID genes include nine with loss-of-function mutations(ABI2, MAPK8, MPDZ, PIDD1, SLAIN1, TBC1D23, TRAPPC6B, UBA7,andUSP44),and missense mutations include the first reports of variants inBDNForTET1associated with ID. The genes identified also showed overlap withde novogene sets for other neuropsychiatric disorders. Transcriptional studies showed prominent expression in the prenatal brain. The high yield of AR mutations for ID indicated that this approach has excellent clinical potential and should inform clinical diagnostics, including clinical whole exome and genome sequencing, for populations in which consanguinity is common. As with other AR disorders, the relevance will also apply to outbred populations.
Decoding Single Molecule Time Traces with Dynamic Disorder
Authors: Hwang Wonseok , Lee Il-Buem , Hong Seok-Cheol , Hyeon Changbong
Published: December 2016

Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted dynamic disorder in certain classes of biomolecules, whose dynamic pattern of conformational transitions is affected by slower transition dynamics of internal state hidden in a low dimensional projection. A systematic means to analyze such data is, however, currently not well developed. Here we report a new algorithm – Variational Bayes-double chain Markov model (VB-DCMM) – to analyze single molecule time trajectories that display dynamic disorder. The proposed analysis employing VB-DCMM allows us to detect the presence of dynamic disorder, if any, in each trajectory, identify the number of internal states, and estimate transition rates between the internal states as well as the rates of conformational transition within each internal state. Applying VB-DCMM algorithm to single molecule FRET data of H-DNA in 100 mM-Na+solution, followed by data clustering, we show that at least 6 kinetic paths linking 4 distinct internal states are required to correctly interpret the duplex-triplex transitions of H-DNA.

Author Summary

We have developed a new algorithm to better decode single molecule data with dynamic disorder. Our new algorithm, which represents a substantial improvement over other methodologies, can detect the presence of dynamic disorder in each trajectory and quantify the kinetic characteristics of underlying energy landscape. As a model system, we applied our algorithm to the single molecule FRET time traces of H-DNA. While duplex-triplex transitions of H-DNA are conventionally interpreted in terms of two-state kinetics, slowly varying dynamic patterns corresponding to hidden internal states can also be identified from the individual time traces. Our algorithm reveals that at least 4 distinct internal states are required to correctly interpret the data.
VIP36 preferentially binds to core-fucosylated N-glycans: a molecular docking study
Authors: Fiedler Klaus
Published: December 2016

Alpha 1-6 fucosyltransferase (Fut8) is known for its properties as an enhancer of nonsmall cell lung cancer metastasis and as a suppressor in hepatocellular carcinoma cells (Hep3B). Promising candidates of affected molecules include E-cadherin. In its absence, during epithelial-mesenchymal transition, the pathway triggers signaling to the nucleus via β-catenin-TCF/LEF. Contrarily, in less metastatic tumors, Fut8 stimulates cell-cell adhesion. Regulated classes of molecules could also include the sorting machinery of polarized epithelial cells, sorted ligands or both, that may be altered in cellular transformation. I have analyzed here the cargo receptor VIP36 (Vesicular-integral membrane protein of 36 kD) for carbohydrate interaction. It has been described as a lectin in the ERGIC (endoplasmic reticulum-Golgi intermediate compartment), Golgi apparatus and plasma membrane. The docking reveals top-interacting carbohydrates of the N-glycan and O-glycan class that encompass N-linked glycans of high mannose and equally complex type which likely function as sorted ligands in epithelial cells. O-glycans score lower and include core 2 residue binding. I show that fucose core modifications by Fut8 stimulate binding of N-linked glycans to VIP36, which is known to be different from binding of galectins 3 and 9. This suggests that Fut8-upregulation may directly alter the affinity of sorted cargo and may enhance the sorting to the apical pathway as exemplified in hepatocytes and traffic to bile. High affinity binding of the ganglioside GM1 carbohydrate headgroup to VIP36 suggests a linkage with protein and glycosphingolipid apical transfer in epithelial cells. Thus, this fundamental approach with large scale docking of 165 carbohydrates including 19 N-glycan high mannose, 17 Nglycan hybrid, 9 N-glycan complex, 17 O-glycan core, 27 Sialoside, 25 Fucoside and 51 other glycan residues suggests, that linked cargo-receptor apical transport may provide a path to epithelial polarization that may be modulated by core fucosylation.
Neural dynamics at successive stages of the ventral visual stream are consistent with hierarchical error signals
Authors: Issa Elias B. , Cadieu Charles F. , DiCarlo James J.
Published: December 2016

Ventral visual stream neural responses are dynamic, even for static image presentations. However, dynamical neural models of visual cortex are lacking as most progress has been made modeling static, time-averaged responses. Here, we studied population neural dynamics during face detection across three cortical processing stages. Remarkably, ~30 milliseconds after the initially evoked response, we found that neurons in intermediate level areas decreased their preference for faces, becoming anti-face preferring on average even while neurons in higher level areas achieved and maintained a face preference. This pattern of hierarchical neural dynamics was inconsistent with extensions of standard feedforward circuits that implemented recurrence within a cortical stage. Rather, recurrent models computing errors between stages captured the observed temporal signatures. Without additional parameter fitting, this model of neural dynamics, which simply augments the standard feedforward model of online vision to encode errors, also explained seemingly disparate dynamical phenomena in the ventral stream.
Mobile introns shape the genetic diversity of their host genes
Authors: Repar Jelena , Warnecke Tobias
Published: December 2016

Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data fromSaccharomyces cerevisiae, Schizosaccharomyces pombe, andLachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron. Through multiple lines of evidence we rule out relaxed purifying selection as the cause of uneven nucleotide diversity. Instead, our findings implicate intron mobility as a direct driver of host gene diversity. We discuss two mechanistic scenarios that are consistent with the data: either endonuclease activity and subsequent error-prone repair have left a mutational footprint on the insertion environment of mobile introns or non-random patterns of genetic diversity are caused by exonic co-conversion, which occurs when introns spread to empty target sites via homologous recombination. Importantly, however, we show that exonic co-conversion can only explain diversity gradients near intron-exon boundaries if the conversion templates comes from outside the population. In other words, there must be pervasive and ongoing horizontal gene transfer of self-splicing introns into extant fungal populations.
Import and Export of Gold Nanoparticles: Exchange Rate in Cancer Cells and Fibroblasts
Authors: Ivošev Vladimir , Jiménez Sánchez Gloria , Abi Haidar Darine , Bazzi Rana , Roux Stéphane , Lacombe Sandrine
Published: December 2016

Cancer is one of the leading causes of death. Radiation therapy is an important modality used in cancer treatment being highly cost-effective. Major flaw of radiotherapy is lack of selectivity between cancerous and healthy tissues. Amelioration of radiotherapy by using high-Z nanoparticles as radiation enhancers is one of potential solutions. Gold nanoparticles (AuNPs) are commonly used as radioenhancers. Understanding the interaction between cancer cells and AuNPs is essential in order to achieve best possible radioenhancing effects, while sparing healthy tissues. This work aims to elucidate interactions of ultrasmall (core size: 2.4 nm and hydrodynamic diameter (Dh): 4.5 nm) fluorescently labeled AuNPs with various human cell lines. In this perspective we measured uptake dynamics, characterized route of internalization and time of intracellular retention in various cancer cell lines and fibroblasts. Our results show that uptake dynamics and internalization pathways are strongly cell line-dependant. We also demonstrate that higher proportion of internalized nanoparticles resides in cancer cells, compared to fibroblasts, inin vitroconditions. This work highlights great complexity of cancerous cells and underlines the necessity for excellent knowledge of biological behaviour for each type of cancer. It also emphasizes the major effort needed for efficient cancer treatments and makes an appeal for further development of highly selective nanoparticles in order to hasten their utilization in clinical conditions.
Development of synchrotron X-ray micro-tomography under extreme conditions of pressure and temperature
Authors: Álvarez-Murga M. , Perrillat J. P. , Le Godec Y. , Bergame F. , Philippe J. , King A. , Guignot N. , Mezouar M. , Hodeau J. L.
Published: December 2016

X-ray tomography is a non-destructive three-dimensional imaging/microanalysis technique selective to a wide range of properties such as density, chemical composition, chemical states and crystallographic structure with extremely high sensitivity and spatial resolution. Here the development ofin situhigh-pressure high-temperature micro-tomography using a rotating module for the Paris–Edinburgh cell combined with synchrotron radiation is described. By rotating the sample chamber by 360°, the limited angular aperture of ordinary high-pressure cells is surmounted. Such a non-destructive high-resolution probe provides three-dimensional insight on the morphological and structural evolution of crystalline as well as amorphous phases during high pressure and temperature treatment. To demonstrate the potentials of this new experimental technique the compression behavior of a basalt glass is investigated by X-ray absorption tomography, and diffraction/scattering tomography imaging of the structural changes during the polymerization of C60molecules under pressure is performed. Small size and weight of the loading frame and rotating module means that this apparatus is portable, and can be readily installed on most synchrotron facilities to take advantage of the diversity of three-dimensional imaging techniques available at beamlines. This experimental breakthrough should open new ways forin situimaging of materials under extreme pressure–temperature–stress conditions, impacting diverse areas in physics, chemistry, geology or materials sciences.
OH cleavage from tyrosine: debunking a myth
Authors: Bury Charles S. , Carmichael Ian , Garman Elspeth F
Published: December 2016

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C—O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr –OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr –OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr –OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr –OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.
Linear parabolic single-crystal diamond refractive lenses for synchrotron X-ray sources
Authors: Terentyev Sergey , Polikarpov Maxim , Snigireva Irina , Di Michiel Marco , Zholudev Sergey , Yunkin Vyacheslav , Kuznetsov Sergey , Blank Vladimir , Snigirev Anatoly
Published: December 2016

Linear parabolic diamond refractive lenses are presented, designed to withstand high thermal and radiation loads coming from upgraded accelerator X-ray sources. Lenses were manufactured by picosecond laser treatment of a high-quality single-crystal synthetic diamond. Twelve lenses with radius of curvature at parabola apex R = 200 µm, geometrical aperture A = 900 µm and length L = 1.5 mm were stacked as a compound refractive lens and tested at the ESRF ID06 beamline. A focal spot of size 2.2 µm and a gain of 20 were measured at 8 keV. The lens profile and surface quality were estimated by grating interferometry and X-ray radiography. In addition, the influence of X-ray glitches on the focusing properties of the compound refractive lens were studied.
{2-[Bis(2,4-di-tert-butylphenoxy)phosphanyloxy-κP]-3,5-di-tert-butylphenyl-κC1}{3,3′-di-tert-butyl-5,5′-dimethoxy-2,2′-bis[(1,1,2,2-tetraphenylethane-1,2-dioxy)phosphanyloxy-κP]biphenyl}rhodium(I) toluene-d82.7-solvate
Authors: Selent Detlef , Spannenberg Anke , Börner Armin
Published: December 2016

The molecule of the title compound, [Rh(C42H62O3P)(C74H68O4P2]·2.7C7D8, consists of two phospharhodacyclic substructures sharing the Rh atom, which are formed by coordination/ortho-metallation of a triaryl phosphite, and by the coordination of a rigid bisphosphite, respectively. The metal displays a tetrahedrally distorted square-planar coordination geometry. Atert-butyl group shows rotational disorder over two positions with refined site occupancy of 0.561 (3):0.439 (3). Two partial-occupancy toluene solvent molecules are disordered over two orientations with site occupancies of 0.5:0.3 and 0.5:0.4, respectively. Intramolecular C—H...O hydrogen bonds are observed. In the crystal, complex molecules and toluene solvent molecules pack as alternating layers parallel to theacplane.
3-Methoxy-4-(prop-2-yn-1-yloxy)benzaldehyde
Authors: Ezhilarasu Tamilarasu , Balasubramanian Sengottuvelan
Published: December 2016

In the title compound, C11H10O3, the prop-2-yn-1-yl group is inclined to the benzene ring by 69 (7)°. In the crystal, molecules are linked by a pair of C—H...O hydrogen bonds, forming inversion dimers with anR22(12) ring motif. The dimers are linked by a second C—H...O hydrogen bond, forming sheets parallel to the (102) plane. The sheets stack along thec-axis direction with a separation ofca3.4 Å.
A monoclinic polymorph of 2-(4-nitrophenyl)acetic acid
Authors: Kennedy Alan R. , Silva de Moraes Lygia
Published: December 2016

A new monoclinic form of 4-nitrophenylacetic acid, C8H7NO4, (I), differs from the known orthorhombic form both in its molecular conformation and in its intermolecular contacts. The conformation is different as the plane of the carboxylic acid group in (I) is more nearly perpendicular to the plane of the aromatic ring [dihedral angle = 86.9 (3)°] than in the previous form (74.5°). Both polymorphs display hydrogen-bondedR22(8) carboxylic acid dimeric pairs, but in (I), neighbouring dimers interact through nitro–nitro N...O dipole–dipole contacts rather than the nitro–carbonyl contacts found in the orthorhombic form.
Methyl 2-(benzoyloxy)benzoate
Authors: Naveen P. , Naveen S. , Zabiulla  , Benaka Prasad S. B. , Lokanath N. K. , Khanum Shaukath Ara , Warad Ismail
Published: December 2016

In the title compound, C15H12O4, the arene rings are inclined at an angle of 65.97 (6)°. The pendant methyl ester substituent has an extended conformation. In the crystal, molecules are linked by C—H...π interactions, forming chains propagating along theb-axis direction. The chains are linkedviaoffset π–π interactions [intercentroid distance = 3.640 (1) Å], forming sheets parallel to (10-1).
2-Amino-5-bromopyridinium 2-phenoxyacetate
Authors: Dhanabalan Nallathambi , Thanigaimani Kaliyaperumal , Khalib Nuridayanti Che , Santhanaraj K. Joseph , Razak Ibrahim Abdul
Published: December 2016

The phenoxyacetate anion of the title salt, C5H6BrN2+·C8H7O3−, is essentially planar, with a dihedral angle of 7.6 (5)° between the carboxylate group and the benzene ring. In the crystal, the cation and the anion are linkedviaN—H...O hydrogen bonds, forming a helical chain along a 21screw axis. In the chain, a π–π stacking interaction between the pyridinium and benzene rings, with a centroid–centroid distance of 3.854 (2) Å, and a C—H...O interaction are observed. The chains are further linked through another C—H...O hydrogen bond, forming a three-dimensional network.
3-Methyl-4,5,6,7,8,9-hexahydrocycloocta[d][1,2,3]selenadiazol]-3-ium iodide triiodide (3/2/1)
Authors: Schollmeyer Dieter , Detert Heiner
Published: December 2016

The title compound, 3C9H15N2Se+·I3−·2I−, was prepared by methylation of the selenadiazole with methyl iodide. The asymmetric unit is composed of three independent selenadiazolium ions arranged in layers and connectedviaI3−·(I−)2anion layers. The distances between the iodine and selenium atoms are significantly shorter than the nitrogen-to-iodine distances.
catena-Poly[[dichloridomercury(II)]-μ-3,5-bis[2-(pyridin-4-yl)ethynyl]pyridine-κ2N:N′]
Authors: Zhang Peng , Yang Qi , Zhao Minjian
Published: December 2016

In the title coordination polymer, [HgCl2(C19H11N3)]n, the HgIIatom is coordinated by two N atoms of symmetry-related 3,5-bis(pyridin-4-ylethynyl)pyridine ligands (L) and by two chloride ions in a distorted tetrahedral geometry. The dihedral angles between the coordinated pyridine rings and the central pyridine ring are 44.6 (3) and 14.2 (3)°, respectively, while the dihedral angle between the two coordinating pyridine rings is 56.1 (3)°. The ligand bridges the HgIIatoms, forming a zigzag chain running parallel to thebaxis. There are no other significant intermolecular interactions present in the crystal.
Household food waste and eating behavior: empirical survey
Authors: Lanfranchi Maurizio , Calabrò Grazia , De Pascale Angelina , Fazio Alessandro , Giannetto Carlo
Published: December 2016

Purpose

In the food chain the identification of household food wastes represents the most problematic aspect to analyze: both as regards the assessment of its qualitative and quantitative aspects and for the detection of measures to reduce or control its generation. In 2012, in fact, the analyzed area showed an inequality index for disposable income of 6.3, and a relative poverty risk index of 42.3. The paper aims to discuss these issues.

Design/methodology/approach

In order to get deeper insights into consumers’ wasting behaviors, a survey on food waste generation in households was carried out in a province of Sicily (Italy). The questionnaire has been formulated taking into account the socio-demographic characteristics for the person who, in the family, usually makes the expenditure, in particular: gender, age, marital status, number of household members, education level, type (single, with or without children, married with or without children), worker and/or student if responsible for food shopping, the number of monthly meals, the kind of ready meal eaten (frozen, fresh, canned or freeze-dried), net monthly income for the family, etc. (adapted by Baeet al., 2010). The data collected from the statistical return of the consumers were drawn up to transform the same data into information of simpler and more concise interpretation.

Findings

The results of the survey are presented in this paper. They can help understand the reasons for discarding edible food and to identify the food groups that are most wasted.

Research limitations/implications

The analysis of a larger land area or community allows most relevant conclusions. The research has an exploratory perspective since the sample strategy is not probabilistic.

Social implications

The findings could be susceptible to support practical and social implications for the identification of measures and instruments aimed at reducing food waste and at increasing consumers’ awareness on that issue.

Originality/value

The study can stimulate sustainable consumption and consumer behavior especially in light of the current economic crisis.
Effect of product attribute beliefs of ready-to-drink coffee beverages on consumer-perceived value and repurchase intention
Authors: Wang Edward S.-T. , Yu Jia-Rong
Published: December 2016

Purpose

The purpose of this paper is to explore the effect of the product attribute beliefs of ready-to-drink (RTD) coffee beverages (i.e. content sensory, packaging and branding, and content functional attributes) on perceived value (i.e. utilitarian and hedonic value) and repurchase intention.

Design/methodology/approach

In the study survey, 401 participants who had purchased RTD coffee beverages within the previous month were included. Structural equation modelling was employed to analyse the survey data.

Findings

The findings indicate that consumers of RTD coffee beverages form utilitarian and hedonic value perceptions through content sensory, packaging and branding, and content functional attribute beliefs. Furthermore, utilitarian value is one of the most crucial determinants of repurchase intentions. The findings further reveal that whereas content functional attribute beliefs have a dominant influence on utilitarian value, content sensory attribute beliefs have a greater influence on hedonic value.

Originality/value

The findings of this study can serve as a reference for RTD coffee beverage companies to develop new products and communication strategies.
“They said I’m a square for eating them”
Authors: Povey Rachel , Cowap Lisa , Gratton Lucy
Published: December 2016

Purpose

The purpose of this paper is to explore primary school children’s beliefs towards eating fruit and vegetables in a deprived area in England.

Design/methodology/approach

Semi-structured interviews were conducted with 11 children aged 9-11 from an after school club at a primary school in a deprived area in the West Midlands. Interviews were analysed using inductive thematic analysis.

Findings

Six master themes emerged from the data: “effect on the senses”, “feelings about food”, “healthy vs unhealthy foods”, “effects on health”, “convenience” and “family and friends”. Analysis showed that children seemed to have a very good awareness of the health benefits of eating fruit and vegetables. However, negative beliefs were associated with sensory perceptions (such as taste, texture, appearance and aroma), availability, and the competing desirability of other, unhealthy foods. Also, although parents were key influences, siblings and friends were often perceived as negative influences and would tease children about eating fruit and vegetables.

Practical implications

Suggestions for interventions include increasing the appeal and availability of pre-prepared fruits and vegetables in both home and school environments. Additionally, an approach to eating more fruit and vegetables which focusses on siblings and friends is advocated as these groups appear to play a key role in terms of promoting the consumption of these foods.

Originality/value

This study is novel as it uses individual interviews to explore primary school children’s attitudes towards fruit and vegetable consumption in a deprived area in England. By focussing on the specific behaviours of fruit and vegetable consumption, the findings aid the development of interventions that are designed to improve children’s healthy eating behaviour.
Exploring key service quality dimensions at a winery from an emerging market’s perspective
Authors: Lee Kyuho , Madanoglu Melih , Ko Jae-Youn
Published: December 2016

Purpose

The purpose of this paper is to uncover the service quality dimensions that influence satisfaction with wineries and future intentions to return among Chinese consumers. With the rapidly growing popularity of wine consumption among Chinese consumers, an increasing number of Chinese consumers are visiting wineries in Western countries. However, while substantial research about wine tourism in Western countries has been published, there is very little research available with respect to wine tourism in China and the Chinese winery visitors who visit them.

Design/methodology/approach

A convenience sampling method was selected. Specifically, snowball sampling was used to collect the study’s data due to the limited number of Chinese consumers who drink wine and who have been involved with wine tourism. Research assistants who speak Chinese fluently used snowball sampling to recruit Chinese consumers in Yentai region who had participated in wine tourism in the past and asked them to complete the research survey. The research assistants distributed 200 surveys through a snowball sampling and collected a total of 179 responses.

Findings

The study’s results suggest that wine tasting operations, such as a variety of wines at tasting room tastings, and the quality of the wines tasted, along with staff attitudes are critical components that influence Chinese wine tourists’ satisfaction and loyalty.

Research limitations/implications

The major contribution of this paper is that it builds on extant wine tourism literature by providing insights into the characteristics of Chinese wine tourists. The paper also illuminates the linkage between winery service quality attributes and Chinese wine tourists’ satisfaction and loyalty.

Practical implications

The results of the study provide a useful guide to both academics and winery operators interested in developing a competitive winery service quality strategy for Chinese wine tourists.

Originality/value

Given the scarcity of literature linking winery service quality attributes and Chinese wine tourists’ satisfaction and loyalty, this study is one of the few studies to explore this relationship.
Perceptions of food labelling about allergens in food products in South Korea
Authors: Choi Jinkyung , Choi Ahyeon
Published: December 2016

Purpose

Allergy information on food labels is crucial to individuals with food allergies. The purpose of this paper is to investigate what information consumers are concerned with as well as improving the allergen information on the product labels.

Design/methodology/approach

A questionnaire was developed based on previous studies and was administered to citizens in South Korea. Descriptive analysis and analysis of variance were conducted to find significances of important information when purchasing and improvement needed on the labels in relation to allergy knowledge.

Findings

The results indicated that respondents were concerned about allergy information and general information regarding the basic value of food and also food safety. In addition, this study found knowledge of food allergies is not related to consideration of allergy information on labels.

Originality/value

This study measured consumers’ perceptions of the current food allergy labeling when purchasing food products. This study concluded improvements were needed in order to deliver allergy information in a clear manner. Such as font size, shape, and color should be implemented together in order to communicate effectively with allergic consumers.
Word associations with “organic”: what do consumers think of?
Authors: Hilverda Femke , Jurgens Manon , Kuttschreuter Margot
Published: December 2016

Purpose

The purpose of this paper is to examine the word associations that consumers have with organic food, organic meat or organic vegetables, and how these associations differ between food type and consumer groups. Construal-level theory was used as a theoretical framework to interpret the associations. In addition, consumer groups were compared on psychological distance, values, age, and gender.

Design/methodology/approach

Two studies were performed. In Study 1, a sample of 154 participants filled out the words that came to their mind when thinking of organic food, organic meat or organic vegetables, and psychological distance and values were measured. In Study 2 these words were rated on centrality by an independent sample (n=52).

Findings

Consumers think of animal welfare, price, health, pesticides, and naturalness the most when thinking of organic. The environment, health, honesty, pesticides, sustainability, quality, natural, additives, origin, certification, and taste were central across organic food, organic meat, and organic vegetables. Thinking of organic meat showed consumers’ concern for animal welfare, while thinking of organic vegetables showed concern for human health. Consumer groups differed regarding psychological distance, values, gender, and age. Consumers who frequently bought organic food were more positive about organic food products compared to consumers who occasionally or hardly ever bought organic food products.

Originality/value

This research extends the scope of current consumer research about organic food and provides new insight in the word associations consumers have with organic food products.
Perceptions and attitudes of the Mexican urban population towards genetically modified organisms
Authors: López Montesinos Osval A. , Pérez Emeterio Franco , Fuentes Eric Eduardo Santos , Luna-Espinoza Ignacio , Cuevas Flavio Aragón
Published: December 2016

Purpose

The purpose of this paper is to measure Mexicans’ perceptions and attitudes about the production and consumption of genetically modified organisms (GMOs).

Design/methodology/approach

A questionnaire with 63 questions that encompassed 11 latent factors was used to obtain information. The questionnaire was administered to 14,720 people in Mexico’s urban areas.

Findings

The results revealed important similarities and differences with studies in other countries, showing mainly that the respondents did not have sufficient information about GMOs, they have low level of knowledge about GMOs (31.28 percent), are highly distrustful of GMOs, perceive high risk regarding GMOs (59.13 percent), want transgenic products to be labeled (93.59 percent) and do not perceive GMOs’ social values and positive health effects beyond increasing agricultural productivity. Also, it was observed that the higher the educational level of individuals, the lower the acceptance of GMOs.

Research limitations/implications

The authors conclude that it is necessary to generate and provide scientifically accurate information on GMOs, so that people are better informed and can give a critical opinion on the use of GMOs.

Practical implications

The major practical contribution of this research is that it provides empirical knowledge about the perceptions and attitudes toward the production and consumption of GMOs among the Mexican’s urban society, which can be of great help for the Mexican government to rethink if it is an appropriate moment to completely open the doors to international companies to cultivate crops like maize and others that have been postponed due to pressure from the environmental groups, farmers and other sectors of the society.

Social implications

This is especially important in the context of maize as it is part of the cultural heritage of Mexico since ancient times. However, it is not clear what the overall perception is in the Mexican society on the use of GMOs for cultivation.

Originality/value

Southern regions of Mexico are the center of origin of several cultivated plants such as maize and legumes. The introduction of GMOs, called transgenics, in agriculture and food continues to cause enormous controversy in the perceptions and attitudes mainly among environmental groups and farmers in Mexico.
Solid Africa’s industrial kitchen: the dilemma
Authors: Muziramakenga Lionel , Abe Masato , Landi James
Published: December 2016

Subject area

Capital budgeting and investment.

Study level/applicability

Undergraduate level.

Case overview

Ms Kamariza, a young Rwandan citizen, established the non-profit organization “Solid Africa” in December 2010. She created the organization together with young professionals, friends and family members with the aim of supporting the most socioeconomically vulnerable individuals’ needs for medical, hygiene, emotional and food services. Ms Kamariza became the Chief Executive Officer and her sister the Chief Financial Officer; together with the help of other additional volunteer staff they carry out this important work. The founders have done an excellent job of maintaining the organization for five years, feeding an average of 1,000 patients every day, and gaining widespread favorable reputation. However, the organization has heavily relied on donations through fundraising events and member contributions (currently 148 members). In 2011, the founders decided that the organization should become self-reliant by planning to build an industrial kitchen, which would cater to different companies (new customers) while also providing free meals to socioeconomically vulnerable patients. This kitchen is foreseen to continuously generate revenue and profits.

Expected learning outcomes

The case is aimed at undergraduate students, pursuing their bachelor, management or social science studies. The teaching is mainly suited for students focused in the fields of social entrepreneurship, finance and social innovation. Students should be able to demonstrate the challenges faced by social entrepreneurs in their quest for capital investment; they should understand how management biases can affect business decision-making; they should also demonstrate the importance of capital budgeting techniques in a social enterprise to achieve better investment decision-making.

Supplementary materials

Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code

CSS 3: Entrepreneurship.
Hybrid publishing design methods for technical books
Authors: Silva Ana Catarina , Borges Maria Manuel
Published: December 2016

Purpose

The purpose of this paper is to provide a characterization of the editorial design methods of technical books in a hybrid publishing context.

Design/methodology/approach

The paper starts by characterizing editorial design as a discipline itself within graphic design, which is then further identified as in urgent need to adapt strategies to technologies, communication processes and existing information flows. Along with the literature review, the paper includes an analysis of one particular case study, O’Reilly Media.

Findings

The paper provides arguments to conclude that the classical approach to the designer’s workflow should be reviewed and the way of framing the editorial problem should also be different: it should focus on the content.

Originality/value

The paper includes implications for the improvement of digital workflows and design processes in the STM hybrid publishing field.