bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the influence of silicone elastomer properties on wedge-shaped microstructured dry adhesives loaded in shear
Authors: Simaite Aiva , Temple Brigitte , Amin Karimi Mohammad , Alizadehyazdi Vahid , Spenko Matthew
Published: September 2018

Anisotropic, gecko-inspired, microstructured adhesives are one of the most promising solutions for many applications in robotics and biomedical applications that require controllable adhesives to grip flat surfaces. In such adhesives, normal adhesion is negligible when loaded solely in the normal direction, but becomes available when the adhesive is loaded in shear first. However, much remains to be learned regarding the friction and failure mechanisms of microstructures loaded in shear. In response, we analysed the load–displacement profiles of wedge-shaped microstructured adhesives comprised of nine different silicone elastomers and their mixtures loaded in shear. The results show that the friction profile depends on at least three factors related to material properties: interfacial adhesion strength in the normal direction (work of separation), elastic modulus and the sample's imperfections (e.g. contamination, misalignment and moulding errors). Moreover, the work of separation influences the maximum friction load such that for materials with the same elastic modulus, the strongest interfacial adhesion yields the lowest friction force. To explain this, we suggest that strongly adhering materials will lead to a macroscopic frictional sliding of the array rather than previously reported stick-slip behaviour.
‘Homoeopathy flourishes in the far East’: A forgotten history of homeopathy in late nineteenth-century China
Authors: Lu Di
Published: September 2018

Homeopathy and its transnational transmission have received significant attention from historians of medicine. But the emergence of homeopathy in modern Chinese society has remained little explored. This article identifies the homeopathic practitioners arriving in nineteenth-century China, and then explores their origins, efforts and sense of professional identity in a transnational context. The history of homeopathy in China is found to begin in the late nineteenth century, during which the growth of the Christian missionary enterprise promoted the arrival of sporadic Euro-American homeopathic practitioners, also missionaries, in coastal regions of China. Almost all of them received professional training in American homeopathic medical institutions; and most of them were females, providing additional opportunities for local women patients to receive treatment. The practitioners recognized homeopathy and their collective homeopathic identity, but their healing services were not necessarily essentially homeopathic. Homeopathy that they learnt also evolved and transacted with exotic knowledge during its globalization. Under the influence of homeopathy, some Euro-Americans claimed to have discovered homeopathic elements in Chinese medical ideas and practice. The early history of homeopathy explored in this article helps deconstruct the popular imagination of a coherent ‘Western medicine’ in modern China.
Fractal kinetic characteristics of hard-rock uranium leaching with sulfuric acid
Authors: Zeng Sheng , Li Jinzhu , Tan Kaixuan , Zhang Shuwen
Published: September 2018

In order to study the fractal dynamic properties of uranium leach mining and discuss the influence of ore crushing on the dynamics of leach mining, uranium mine ore rocks in southern China were selected as the research object and an acid leaching experiment was performed on the ore samples with different fractal dimensions of 1.1, 1.4, 1.7, 2.0, 2.3 and 2.6. In the column leaching experiment, a PVC pipe with an inner diameter of 112 mm and a height of 1500 mm was used. The uranium content was determined by using titanium trioxide that was placed into a 0.1 mg ml
−1
standard uranium solution, and a sampling rate of once daily with a 5 ml volume of leaching solution was adopted after 8 h drenching time. The results show that the flow rate of the leaching solution depends on the distribution of the ore's particle size, that is, a larger fractal dimension results in a smaller flow rate. The concentration of the uranium leaching solution reaches a maximum value which subsequently decreases with time on the third day of the experiment, and it seems that the changes in the uranium concentration tend to be stable at around 15 days. Moreover, the concentration seems to increase with the increasing fractal dimension, and the fractal dimension of the ore particle size has a significant impact on the leaching kinetics. When the fractal dimension is between 1.1 and 2.6, the uranium dissolution rate,
K
, increases with the increasing fractal dimension. The kinetic reaction of the uranium leaching is a liquid–solid one, which is controlled by chemical reactions in the earlier phase. While the middle reaction phase is mainly chemical-diffusion reaction coupling, and the latter part of the reaction is controlled by diffusion. As the fractal dimension increases, the liquid–solid reaction controlled by diffusion appears at earlier phases. When the fractal dimension is greater than 2.0, the time of entering the diffusion control phase only changed little with the increasing of the fractal dimension. At last, a fractal dimension of 2.0 is suggested for the acid leaching of uranium ore crushing.
Impact of support characteristics and preparation method on photocatalytic activity of TiO
2
/ZSM-5/silica gel composite photocatalyst
Authors: Radwan Emad K. , Langford Cooper H. , Achari Gopal
Published: September 2018

Titanium dioxide (Degussa P25) was supported onto two different aluminosilicate zeolites (ZSM-5) and anchored on three silica gels using two separate preparation methods to study the effect of the catalyst components and the preparation method on the photoactivity of composite catalysts. The photoactivity was investigated by tracking phenol disappearance in a batch UVA light-emitting diode reactor. An easily separable photocatalyst with higher photoactivity than commercial Degussa P25 was developed using Degussa P25, ZSM-5 (SiO
2
/Al
2
O
3
= 280) and silica gel (particle size 0.2–0.5 mm and pore size 40 Å). The optimum composition was found to be P25:ZSM-5:silica gel = 0.3 : 0.5 : 0.5 g l
−1
. SEM photographs show that the distribution of the composite catalyst components prepared without a binder was better than that prepared with a binder. The efficiency of photocatalytic ozonation of sulfamethoxazole (SMX) using the new photocatalyst was assessed and compared to that of commercially available Degussa P25. It was found that photocatalytic ozonation promoted the SMX disappearance and mineralization. PZS was superior to Degussa P25 with respect to photocatalysis and photocatalytic ozonation. The enhancement was attributed to the synergetic effect between adsorption, ozonation and/or photocatalytic oxidation.
Hydrodynamic performance of suction feeding is virtually unaffected by variation in the shape of the posterior region of the pharynx in fish
Authors: Provini Pauline , Van Wassenbergh Sam
Published: September 2018

To capture prey by suction, fish generate a flow of water that enters the mouth and exits at the back of the head. It was previously hypothesized that prey-capture performance is improved by a streamlined shape of the posterior region of the pharynx, which enables an unobstructed outflow with minimal hydrodynamic resistance. However, this hypothesis remained untested for several decades. Using computational fluid dynamics simulations, we now managed to quantify the effects of different shapes of the posterior pharynx on the dynamics of suction feeding, based on a feeding act of a sunfish (Lepomis gibbosus). In contrast to what was hypothesized, the effects of the imposed variation in shape were negligible: flow velocity patterns remained essentially identical, and the effects on feeding dynamics were negligibly small. This remarkable hydrodynamic insensitivity implies that, in the course of evolution, the observed wedge-like protrusions of the pectoral surfaces of the pharynx probably resulted from spatial constraints and/or mechanical demands on the musculoskeletal linkages, rather than constraints imposed by hydrodynamics. Our study, therefore, exceptionally shows that a streamlined biological shape subjected to fluid flows is not always the result of selection for hydrodynamic improvement.
Identifying Changes to RNA Editome in Major Depressive Disorder
Authors: Hasan Saam , Robbani Shahriyar Mahdi , Afroze Tamanna , Ahsan Giasuddin , Hossain Muhammad Maqsud
Published: September 2018

Major Depressive Disorder (MDD) is one of the most significant psychiatric disorders in the world today. Its incidence is widespread in society and its heavy adverse impact on the quality of life is well documented. Previously genetic studies on MDD had identified a hereditary component of the disease as well as crediting RNA editing with a role in its development. The later due to an overexpression of a heavily edited isoform of the Serotonin 2c receptor. Here we used publicly available RNA sequence data from suicide patients diagnosed with MDD as well as controls for identifying RNA editing sites unique to MDD. After variant calling and several steps of filtering, we identified 142 unique RNA editing sites in the MDD patients. These included intronic, downstream, UTR3 and exonic edits. The latter comprising several amino acid changes in the encoded protein. The genes implicated to be uniquely edited in MDD included the aforementioned and previously implicated Serotonin 2c receptor, others involved in functions that play roles in depression and suicide such as Cannabinoid Receptor 1, Frizzled Class 3 Receptor, Neuroligin 3 and others.
Localization of balanced chromosome translocation breakpoints by long-read sequencing on the Oxford Nanopore platform
Authors: Hu Liang , Liang Fan , Cheng Dehua , Zhang Zhiyuan , Yu Guoliang , Zha Jianjun , Wang Yang , Wang Feng , Tan Yueqiu , Wang Depeng , Wang Kai , Lin Ge
Published: September 2018

Structural variants (SVs) in genomes, including translocations, inversions, insertions, deletions and duplications, remain difficult to be detected reliably by traditional genomic technologies. In particular, balanced translocations and inversions cannot be detected by microarrays since they do not alter chromosome copy numbers; they cannot be reliably detected by short-read sequencing either, since many breakpoints are located within repetitive regions of the genome that are unmappable by short reads. However, the detection and the precise localization of breakpoints at the nucleotide level are important to study the genetic causes in patients carrying balanced translocations or inversions. Long-read sequencing techniques, such as the Oxford Nanopore Technology (ONT), may detect these SVs in a more direct, efficient and accurate manner. In this study, we applied whole-genome long-read sequencing on the Oxford Nanopore GridION sequencer to detect the breakpoints from 6 carriers of balanced translocations and one carrier of inversion, where SVs had initially been detected by karyotyping at the chromosome level. The results showed that all the balanced translocations were detected with ∼10X coverage and were consistent with the karyotyping results. PCR and Sanger sequencing confirmed 8 of the 14 breakpoints to single base resolution, yet other breakpoints cannot be refined to single-base due to their localization at highly repetitive regions or pericentromeric regions, or due to the possible presence of local deletions/duplications. Our results indicate that low-coverage whole-genome sequencing is an ideal tool for the precise localization of most translocation breakpoints and may provide haplotype information on the breakpoint-linked SNPs, which may be widely applied in SV detection, therapeutic monitoring, assisted reproduction technology (ART) and preimplantation genetic diagnosis (PGD).
Drilling down hotspots of intraspecific diversity to bring them into on-ground conservation of threatened species
Authors: Zampiglia Mauro , Bisconti Roberta , Maiorano Luigi , Aloise Gaetano , Siclari Antonino , Pellegrino Francesco , Martino Giuseppe , Pezzarossa Alice , Chiocchio Andrea , Martino Chiara , Nascetti Giuseppe , Canestrelli Daniele
Published: September 2018

Unprecedented rates of biodiversity loss rise the urgency for preserving species ability to cope with ongoing global changes. An approach in this direction is to target intra-specific hotspots of genetic diversity as conservation priorities. However, these hotspots are often identified by sampling at a spatial resolution too coarse to be useful in practical management of threatened species, hindering the long-appealed dialog between conservation stakeholders and conservation genetic researchers. Here, we investigated the spatial and temporal variation in species presence, genetic diversity, as well as potential risk factors, within a previously identified hotspot of genetic diversity for the endangered Apennine yellow bellied toad Bombina pachypus. Our results show that this hotspot is neither a geographically homogeneous nor a temporally stable unit. Over a time-window spanning 10-40 years since previous assessments, B. pachypus populations declined in large portions of its hotspot, and their genetic diversity levels decreased. Considering the demographic trend, genetic and epidemiological data, and models of current and future climatic suitability, populations at the extreme south of the hotspot area still qualify for urgent in-situ conservation actions, whereas northern populations would be better managed through a mix of in-situ and ex-situ actions. Our results emphasize that identifying hotspot of genetic diversity, albeit essential step, does not suffice to warrant on-ground conservation of threatened species. Hotspots should be analysed at finer geographic and temporal scales, to provide conservation stakeholders with key knowledge to best define conservation priorities, and to optimize resource allocation to alternative management practices.
SpeciesMLP: Sequence based Multi-layer Perceptron for Amplicon Read Classification Using Real-time Data Augmentation
Authors: Kishk Ali , El-Hadidi Mohamed
Published: September 2018

Taxonomic assignment is the core of targeted metagenomics approaches that aims to assign sequencing reads to their corresponding taxonomy. Sequence similarity searching and machine learning (ML) are two commonly used approaches for taxonomic assignment based on the 16S rRNA. Similarity based approaches require high computation resources, while ML approaches do not need these resources in prediction. The majority of these ML approaches depend on k-mer frequency rather than direct sequence, which leads to low accuracy on short reads as k-mer frequency does not consider k-mer position. Moreover training ML taxonomic classifiers depend on a specific read length which may reduce the prediction performance by decreasing read length. In this study, we built a neural network classifier for 16S rRNA reads based on SILVA database (version 132). Modeling was performed on direct sequences using Convolutional neural network (CNN) and other neural network architectures such as Multi-layer Perceptron and Recurrent Neural Network. In order to reduce modeling time of the direct sequences, In-silico PCR was applied on SILVA database. Total number of 14 subset databases were generated by universal primers for each single or paired high variable region (HVR). Moreover, in this study, we illustrate the results for the V2 database model on 8443 classes on the species level and 1552 on the genus level. In order to simulate sequencing fragmentation, we trained variable length subsequences from 50 bases till the full length of the HVR that are randomly changing in each training iteration. Simple MLP model with global max pooling gives 0.71 & 0.93 test accuracy for the species and genus levels respectively (for reads of 100 base sub-sequences) and 0.75 & 0.96 accuracy for the species and genus levels respectively (on the full length V2 HVR). In this study, we present a novel method (SpeciesMLP https://github.com/ali-kishk/SpeciesMLP) to model the direct amplicon sequence using MLP over a sequence of k-mers faster 20 times than CNN in training and 10 times in prediction.
rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
Authors: Bushmanova Elena , Antipov Dmitry , Lapidus Alla , Prjibelski Andrey D.
Published: September 2018

Possibility to generate large RNA-seq datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the model organisms with finished and annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing and paralogous genes. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-Seq datasets, and briefly highlight strong and weak points of different assemblers.

Availability and implementation

rnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.
SplicedFamAlign: CDS-to-gene spliced alignment and identification of transcript orthology groups
Authors: Jammali Safa , Aguilar Jean-David , Kuitche Esaie , Ouangraoua Aïda
Published: September 2018

Motivation

The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. Spliced alignment that consists in aligning a spliced cDNA sequence against an unspliced genomic sequence, constitutes a promising, yet unexplored approach for the identification of splicing orthology relationships. Existing spliced alignment algorithms do not exploit the information on the splicing structure of the input sequences, namely the exon structure of the cDNA sequence and the exon-intron structure of the genomic sequences. Yet, this information is often available for coding DNA sequences (CDS) and gene sequences annotated in databases, and it can help improve the accuracy of the computed spliced alignments. To address this issue, we introduce a new spliced alignment problem and a method called SplicedFamAlign (SFA) for computing the alignment of a spliced CDS against a gene sequence while accounting for the splicing structures of the input sequences, and then the inference of transcript splicing orthology groups in a gene family based on spliced alignments.

Results

The experimental results show that SFA outperforms existing spliced alignment methods in terms of accuracy and execution time for CDS-to-gene alignment. We also show that the performance of SFA remains high for various levels of sequence similarity between input sequences, thanks to accounting for the splicing structure of the input sequences. It is important to notice that unlike all current spliced alignment methods that are meant for cDNA-to-genome alignments and can be used for CDS-to-gene alignments, SFA is the first method specifically designed for CDS-to-gene alignments. We show its usefulness for the comparison of genes and transcripts within a gene family for the purpose of analyzing splicing orthologies. It can also be used for gene structure annotation and alternative splicing analyses.

Availability

SplicedFamAlign was implemented in Python. Source code is freely available at https://github.com/UdeS-CoBIUS/SpliceFamAlign

Contact

safa.jammali@usherbrooke.ca
Rediscovery of red wolf ghost alleles in a canid population along the American Gulf Coast
Authors: Heppenheimer Elizabeth , Brzeski Kristin E. , Wooten Ron , Waddell Will , Rutledge Linda Y. , Chamberlain Michael J. , Stahler Daniel R. , Hinton Joseph W. , vonHoldt Bridgett M.
Published: September 2018

Rediscovering species once thought to be extinct or on the edge of extinction is rare. Red wolves have been extinct along the Gulf Coast region since 1980, with their last populations found in coastal Louisiana and Texas. We report the rediscovery of red wolf ghost alleles in a canid population on Galveston Island, Texas. We analyzed over 7,000 SNPs in 60 canid representatives from all legally recognized North American Canis species and two phenotypically ambiguous canids from Galveston Island. We found notably high Bayesian cluster assignments of the Galveston canids to captive red wolves with extensive sharing of red wolf private alleles. Today, the only known extant wild red wolves persist in a reintroduced population in North Carolina, which is dwindling amongst political and taxonomic controversy. Our rediscovery of red wolf ancestry after almost 40 years introduces both positive opportunities for additional conservation action and difficult policy challenges.
VAPiD: a lightweight cross platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank
Authors: Shean Ryan C. , Makhsous Negar , Stoddard Graham D. , Lin Michelle J. , Greninger Alexander L.
Published: September 2018

Background

With sequencing technologies becoming cheaper and easier to use, more groups are able to obtain whole genome sequences of viruses of public health and scientific importance. Submission of genomic data to NCBI GenBank is a requirement prior to publication and plays a critical role in making scientific data publicly available.

GenBank currently has automatic prokaryotic and eukaryotic genome annotation pipelines but has no viral annotation pipeline beyond influenza virus. Annotation and submission of viral genome sequence is a non-trivial task, especially for groups that do not routinely interact with GenBank for data submissions.

Results

We present Viral Annotation Pipeline and iDentification (VAPiD), a portable and lightweight command-line tool for annotation and GenBank deposition of viral genomes. VAPiD supports annotation of nearly all unsegmented viral genomes. The pipeline has been validated on human immunodeficiency virus, human parainfluenza virus 1-4, human metapneumovirus, human coronaviruses (229E/OC43/NL63/HKU1/SARS/MERS), human enteroviruses/rhinoviruses, measles virus, mumps virus, Hepatitis A-E Virus, Chikungunya virus, dengue virus, and West Nile virus, as well the human polyomaviruses BK/JC/MCV, human adenoviruses, and human papillomaviruses. The program can handle individual or batch submissions of different viruses to GenBank and correctly annotates multiple viruses, including those that contain ribosomal slippage or RNA editing without prior knowledge of the virus to be annotated. VAPiD is programmed in Python and is compatible with Windows, Linux, and Mac OS systems.

Conclusions

We have created a portable, lightweight, user-friendly, internet-enabled, open-source, command-line genome annotation and submission package to facilitate virus genome submissions to NCBI GenBank. Instructions for downloading and installing VAPiD can be found athttps://github.com/rcs333/VAPiD.
Meteorin-like (Metrnl) adipomyokine improves glucose tolerance in type 2 diabetes via AMPK pathway
Authors: Lee Jung Ok , Lee Hye Jeong , Lee Yong Woo , Han Jeong Ah , Kang Min Ju , Moon Jiyoung , Shin Min-Jeong , Lee Ho Jun , Chung Ji Hyung , Lee Jin-Seok , Son Chang-Gue , Song Kwon-Ho , Kim Tae Woo , Lee Eun-Soo , Kim Hong min , Chung Choon Hee , Ngoei Kevin R.W. , Ling Naomi X.Y. , Oakhill Jonathan S. , Galic Sandra , Murray-Segal Lisa , Kemp Bruce E. , Kim Kyoung Min , Lim Soo , Kim Hyeon Soo
Published: September 2018

Meteorin-like (metrnl) is a recently identified adipomyokine that has beneficial effects on glucose metabolism. However, its underlying mechanism of action is not completely understood. In this study, we have shown that a level of metrnl increase in vitro under electrical-pulse-stimulation (EPS) and in vivo in exercise mice, suggesting that metrnl is an exercise-induced myokine. In addition, metrnl increases glucose uptake through the calcium-dependent AMPK pathway. Metrnl also increases the phosphorylation of HDAC5, a transcriptional repressor of GLUT4, in an AMPK-dependent manner. Phosphorylated HDAC5 interacts with 14-3-3 proteins and sequesters them in the cytoplasm, resulting in the activation of GLUT4 transcription. The intraperitoneal injection of recombinant metrnl improves glucose tolerance in mice with high fat-induced obesity or type 2 diabetes (db/db), but this is not seen in AMPK β1β2 muscle-specific null mice (AMPK β1β2 MKO). In conclusion, we have demonstrated that metrnl induces beneficial effects on glucose metabolism via AMPK and is a promising therapeutic candidate for glucose-related diseases such as type 2 diabetes.
Polygenicity of complex traits is explained by negative selection
Authors: O’Connor Luke J. , Schoech Armin P. , Hormozdiari Farhad , Gazal Steven , Patterson Nick , Price Alkes L.
Published: September 2018

Complex traits and common disease are highly polygenic: thousands of common variants are causal, and their effect sizes are almost always small. Polygenicity could be explained by negative selection, which constrains common-variant effect sizes and may reshape their distribution across the genome. We refer to this phenomenon as flattening, as genetic signal is flattened relative to the underlying biology. We introduce a mathematical definition of polygenicity, the effective number of associated SNPs, and a robust statistical method to estimate it. This definition of polygenicity differs from the number of causal SNPs, a standard definition; it depends strongly on SNPs with large effects. In analyses of 33 complex traits (average N=361k), we determined that common variants are ∼4x more polygenic than low-frequency variants, consistent with pervasive flattening. Moreover, functionally important regions of the genome have increased polygenicity in proportion to their increased heritability, implying that heritability enrichment reflects differences in the number of associations rather than their magnitude (which is constrained by selection). We conclude that negative selection constrains the genetic signal of biologically important regions and genes, reshaping genetic architecture.
Penetrance and pleiotropy of polygenic risk scores for schizophrenia in 106,160 patients across four healthcare systems
Authors: Zheutlin Amanda B , Dennis Jessica , Linnér Richard Karlsson , Moscati Arden , Restrepo Nicole , Straub Peter , Ruderfer Douglas , Castro Victor M , Chen Chia-Yen , Ge Tian , Huckins Laura M , Charney Alexander , Lester Kirchner H , Stahl Eli A , Chabris Christopher F , Davis Lea K , Smoller Jordan W
Published: September 2018

OBJECTIVE

Individuals at high risk for schizophrenia may benefit from early intervention but few validated risk predictors are available. Genetic profiling is one approach to risk stratification that has been extensively validated in research cohorts, but its utility in clinical settings remains largely unexplored. Moreover, the broad health consequences of a high genetic risk of schizophrenia are poorly understood, despite being relevant to treatment decisions.

METHOD

We used electronic health records for 106,160 patients from four healthcare systems to evaluate the penetrance and pleiotropy of genetic risk for schizophrenia. Polygenic risk scores (PRSs) for schizophrenia were calculated from summary statistics and tested for association with 1359 disease categories, including schizophrenia and psychosis, in phenome-wide association studies. Effects were combined through meta-analysis across sites.

RESULTS

PRSs were robustly associated with schizophrenia (odds ratio per standard deviation increase in PRS=1.55 [95% confidence interval (CI), 1.4-1.7], p=4.48 x 10-16) and patients in the highest risk decile of the PRS distribution had up to 4.6-fold increased odds of schizophrenia compared to those in the bottom decile (95% CI, 2.9-7.3, p=1.37 x 10-10). PRSs were also positively associated with a range of other phenotypes, including anxiety, mood, substance use, neurological, and personality disorders, as well as suicidal behavior, memory loss, and urinary syndromes; they were inversely related to obesity.

CONCLUSIONS

We demonstrate that an available measure of genetic risk for schizophrenia is robustly associated with schizophrenia in healthcare settings and has pleiotropic effects on related psychiatric disorders as well as other medical syndromes. Our results provide an initial indication of the opportunities and limitations that may arise with the future application of PRS testing in healthcare systems.
Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine
Authors: Maurici Nicole , Savidge Nicole , Lee Byung Uk , Brewer Scott H. , Phillips-Piro Christine M.
Published: September 2018

The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO2F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3221 and the crystal structure was refined to 2.05 Å resolution. Crystals of Asn149pNO2F sfGFP contained one molecule of sfGFP per asymmetric unit in space group P4122 and the structure was refined to 1.60 Å resolution. The alignment of Asp133pNO2F or Asn149pNO2F sfGFP with wild-type sfGFP resulted in small root-mean-square deviations, illustrating that these residues do not significantly alter the protein structure and supporting the use of pNO2F as an effective spectroscopic reporter of local protein structure and dynamics.
Stopping over-medication of people with an intellectual disability, autism or both (STOMP) in England part 2 – the story so far
Authors: Branford David , Gerrard David , Saleem Nigget , Shaw Carl , Webster Anne
Published: September 2018

Purpose

The STOMP programme – stopping the over-medication of people with an intellectual disability, autism or both is a three-year programme supported by NHS England. Concern about the overuse of antipsychotic drugs has been a constant theme since the 1970s. However, despite a multitude of guidelines the practice continues. The report into the events at Winterbourne View not only raised concerns about the overuse of antipsychotic drugs but of antidepressants. Part 1 presented the historical background to the use of psychotropic drugs for people with an intellectual disability, autism or both. The purpose of this paper (Part 2) is to present the approach adopted to reduce over-medication (the “Call to Action”) and the progress so far at the half way stage.

Design/methodology/approach

The “Call to Action” methodology is described in a Manchester University report – mobilising and organising for large-scale change in healthcare “The Right Prescription: A Call to Action on the use of antipsychotic drugs for people with dementia”. Their research suggested that a social mobilising and organising approach to change operates could provide a mechanism for bringing about change where other approaches had failed.

Findings

The adoption of the “Call to Action” methodology has resulted in widespread acknowledgement across intellectual disability practice that overuse of psychotropic medication and poor review was resulting in over-medication. Many individual local programmes are underway (some are described in this paper) however to what extent the overall use of psychotropic drugs has changed is yet to be evaluated.

Originality/value

STOMP is part of an English national agenda – transforming care. The government and leading organisations across the health and care system are committed to transforming care for people with intellectual disabilities autism or both who have a mental illness or whose behaviour challenges services. This paper describes a new approach to stopping the over-medication of people with an intellectual disability, autism or both.
Mental health services for adolescents and adults with intellectual disabilities in Norway: a descriptive study
Authors: Bakken Trine Lise , Evensen Olav Ose , Bjørgen Tale Gjertine , Nilsen Inger Tove , Bang Nina , Pedersen Unni , Berge Kim , Ellingsen Karl Elling , Baasland Terje , Helverschou Sissel Berge
Published: September 2018

Purpose

The purpose of this paper is to present and discuss mental health services for people with intellectual disability (ID) in Norway.

Design/methodology/approach

A literature review and a survey were conducted to map services for people with ID and mental health problems in Norway.

Findings

The results were sparse and confirmed what is already known among clinicians working with these patients. The Norwegian services are fragmented and there are geographical differences.

Research limitations/implications

There are no special services for children with ID developing mental illness. For offenders with ID, a national unit assesses and follows up, also when the person is sentenced to compulsory care and services are provided in their home municipality.

Practical implications

More data about both the patients and the services are needed in order to improve mental health services for people with ID in Norway.

Originality/value

This paper describes mental health services for people with ID in Norway.
Measuring socially responsible consumption: a study of Colombia–Mexico
Authors: Villa Castaño Lida Esperanza , Perdomo-Ortiz Jesús , Durán León William Fernando , Dueñas Ocampo Sebastián , Arredondo Trapero Florina Guadalupe
Published: September 2018

Purpose

The purpose of this paper is to find evidence of construct validity in a Mexican population for a socially responsible consumption (SRC) measurement scale originally proposed for Colombia.

Design/methodology/approach

Using a quantitative approach and a correlational scope, factorial invariance and differential item functioning analyses were performed on the SRC measurement scale based on data from 323 Colombian graduate students and 456 Mexican students.

Findings

The empirical evidence confirms that the factor structure of the SRC measurement scale applied in Colombia remains valid in the Mexican context.

Research limitations/implications

Limitations pertain to the attitudinal measurement scale and the non-representativeness of the chosen samples.

Practical implications

When identifying a structure for SRC, particularly considering the formulation of marketing strategies and business reputation, companies should consider the new criteria of buying consumption.

Originality/value

For the first time in Latin America, an SRC measurement scale is constructed, and its construct validity is evaluated for two countries: Mexico and Colombia. The authors thus provide empirical evidence for the hypothesis that SRC measurement is contingent on the expression of measurement considering the socioeconomic and cultural context in which the study is conducted.
The long-run relationship between farm size and productivity
Authors: Yao Wanjun , Hamori Shigeyuki
Published: September 2018

Purpose

The purpose of this paper is to examine the long-term relationship between farm size and productivity in China at the national level.

Design/methodology/approach

In contrast to the micro-data examination conducted by earlier literature, in this study, the authors use household aggregate panel data on 29 provinces in China for 1988–2012. Using the panel data PMG model, the authors control the factor of difference in land quality due to the fixed effect in each province, and the authors consider the difference in the long-run coefficients of farm size and land productivity rather than the difference in their short-run relationship. Thus, the authors examine the long-term relationship between farm size and productivity. Furthermore, the authors examine the robustness of this relationship in the long-term using samples of rice, wheat and corn production by region.

Findings

In contrast with the findings presented previously, the authors find that the relationship between farm size and agricultural productivity is statistically positive in the long term.

Originality/value

The relationship between farm size and agricultural productivity is a key research issue in agricultural and development economics. In China, many studies have provided evidence of the inverse relationship between farm size and agricultural productivity at the family farm level. However, this inverse relationship seems to reflect specific regions and specific periods in the relationship between farm size and land productivity. At the nationwide level, in the long-term, this is not an inverse but a positive relationship. It is desirable to expand farm size for the long-term development of agriculture.
Is business planning useful for the new venture emergence?
Authors: Wei Ya-long , Long Dan , Li Yao-kuang , Cheng Xu-sheng
Published: September 2018

Purpose

The purpose of this paper is to build a research model to examine the effects of business planning on the new venture emergence, as well as to examine the moderating effects of innovativeness of products.

Design/methodology/approach

Four hypotheses are put forward and examined by hierarchical binary logistic regression. The data of this paper are based on the first two waves of data from Chinese Panel Study of Entrepreneurial Dynamics project.

Findings

Results show that engaging in business planning has a positive effect on the new venture emergence, and the timing of business planning does not affect the new venture emergence significantly. This study also finds that the innovativeness of products has a positive moderating effect on the relationship between the timing of business planning and the new venture emergence.

Research limitations/implications

This study has some limitations. The innovativeness of products is measured by a single indicator, which may not completely reflect the meaning of the attribute. Moreover, this study explores new ventures only in the nascent stage.

Practical implications

The study is useful for entrepreneurs to realize the importance of business planning. First, engaging in business planning in early start-up stage is a very valuable activity, because business planning can help new ventures reduce the loss caused by trial and error learning. Second, engaging in business planning is more likely to ensure high innovative products quickly be accepted by the market. Because in the process of new venture emergence, the legitimacy signal to stakeholders can be transmitted and new products can be promoted to get support and recognition from stakeholder through the business plan.

Originality/value

This paper focuses on the early stage of new venture life cycle and the contextual factors to explore the influence of business planning on the new venture emergence under the logic of legitimacy. This paper could enrich business planning research from the perspective of legitimacy theory by inspiring scholars to focus on the differences between new ventures and mature enterprises and to offer proposals of legitimation strategies suitable for new ventures. Meanwhile, this study contributes to the understanding of the contextual factors of business planning. And it discusses the impact of the attribute in business planning on the new venture emergence, which helps scholars to get a deep thought about the value of business planning in entrepreneurial process.
The influence of properties of printed circuit board resin and filler on drilling force
Authors: Shi Hongyan , Lin Xiaoke , Yan Qiuxin , Zhang JiaNan
Published: September 2018

Purpose

The purpose of this paper is to study and obtain the influence of resin and filler properties of printed circuit board (PCB) on the drilling force during micro drilling.

Design/methodology/approach

Experiments were carried out to study the influence of PCB on micro-hole drilling force under high spindle speed. A drilling force measurement system was applied, and then, the influence of resin and filler properties of PCBs on the force was analyzed. The proportion of resin and filler in the PCB was defined as four levels, and the influence of PCBs based on the drilling force measurement was summarized.

Findings

The drilling force decreased with the decrease in the feed rate, and lower filler (16-30 per cent) and average resin (31-50 per cent) would have a positive impact on the drilling force. At the same time, the size of uniform and fine fillers would help to reduce the drilling force.

Originality/value

The drilling force measurement system was applied, and the influence of PCBs on force was analyzed, which could provide a reference value on the optimization of the drilling force during micro drilling.
Views from the Frontline and Frontline methodology: critical reflection on theory and practice
Authors: Gibson Terry David , Scott Nigel
Published: September 2018

Purpose

The purpose of this paper is to provide a detailed account of the “Views from the Frontline” and “Frontline” methodologies, which underpinned the case studies presented in this issue.

Design/methodology/approach

A participant observer account of the development of the methods, leading to a critical discussion of their deployment and impact and a concluding discussion of further work required.

Findings

The study found that iterative development of the programmes had improved their ability to gather and analyse local experience, knowledge and priorities concerning risk and resilience, but raised a concern over the means by which this information was able to achieve necessary political influence.

Originality/value

This technical paper is a first assessment of the underlying method and application of “Views from the Frontline” and “Frontline” and benefits from the participant observer status of the authors. More work is required on the underlying questions concerning qualitative vs quantitatitive methods, and on the means of achieving political impact from the work.
Library cooperation in Zimbabwe: in search of a suitable model to underpin national development
Authors: Chisita Collence Takaingenhamo , Dick Archie
Published: September 2018

Purpose

The paper explores library cooperation in Zimbabwe and gathers views from librarians on the need for a library consortium model to underpin national development. This study aims to investigate the development of library consortia in Zimbabwe and then propose a model that will both accelerate their development and support the country’s national development agenda.

Design/methodology/approach

The paper opted for an investigative study using a multi-method research design. Data on existing library consortia, namely, Zimbabwe University Library Consortium (ZULC) and College and Research Library Consortium (CARLC), were collected through questionnaires and interviews. The data were complemented by documentary analysis including primary sources of information, for example, annual reports and brochures. Data were analysed qualitatively and quantitatively.

Findings

The paper provides empirical insights on how ZULC and CARLC are transforming the provision of library services in several ways, for example, providing for the dynamic needs of users and strategizing on overcoming rising costs of scholarly content through resource sharing. The proposed model effectively elevates the fundamental library consortium principles of cooperation and sharing onto the national development stage, and it is novel and pioneering. The gestures and general remarks made recently by Zimbabwe Library Association and some ZULC members about national development and ZIMASSET are given rigorous and scholarly expression in this model.

Research limitations/implications

Because of the chosen research approach, the research results may lack generalisability beyond Zimbabwe. It is therefore imperative for researchers to test the proposed propositions further.

Practical implications

The paper includes implications for the development of a library consortia model to underpin national development in Zimbabwe. The existing academic sector library consortium still excludes other types of libraries from participating in resource sharing and promoting access to information on a national development scale. The proposed library consortium model providing for nation-wide access to information is critical in realising national development goals in Zimbabwe. Currently, academic library consortia are contributing immensely through supporting learning, teaching and research in their respective institutions. Such benefits can also be extended to all institutions through a national library consortium to support development in Zimbabwe.

Originality/value

This paper fulfils an identified need to study how the development of a nation-wide library consortium model can be realised. There is relatively little researched information on library cooperation and library consortia and national development in Southern Africa with specific reference to Zimbabwe. The paper seeks to close the gap by providing information on library cooperation and library consortia and national development in Zimbabwe.
Neural networks for determining the vector normal to the surface in CFD, LBM and CA applications
Authors: Svyetlichnyy Dmytro
Published: September 2018

Purpose

The well-known discrete methods of computational fluid dynamics (CFD), lattice Boltzmann method (LBM), cellular automata (CA), volume-of-fluid (VoF) and others rely on several parameters describing the boundary or the surface. Some of them are vector normal to the surface, coordinates of the point on the surface and the curvature. They are necessary for the reconstruction of the real surface (boundary) based on the values of the volume fractions of several cells. However, the simple methods commonly used for calculations of the vector normal to the surface are of unsatisfactory accuracy. In light of this, the purpose of this paper is to demonstrate a more accurate method for determining the vector normal to the surface.

Design/methodology/approach

Based on the thesis that information about the volume fractions of the 3 × 3 cell block should be enough for normal vector determination, a neural network (NN) was proposed for use in the paper. The normal vector and the volume fractions of the cells themselves can be defined on the basis of such variables as the location of the center and the radius of the circumference. Therefore, the NN is proposed to solve the inverse problem – to determine the normal vector based on known values of volume fractions. Volume fractions are inputs of NNs, while the normal vector is their output. Over a thousand variants of the surface location, orientations of the normal vector and curvatures were prepared for volume fraction calculations; their results were used for training, validating and testing the NNs.

Findings

The simplest NN with one neuron in the hidden layer shows better results than other commonly used methods, and an NN with four neurons produces results with errors below 1° relative to the orientation of the normal vector; for several cases, it proven to be more accurate by an order of magnitude.

Practical implications

The method can be used in the CFD, LBM, CA, VoF and other discrete computational methods. The more precise normal vector allows for a more accurate determination of the points on the surface and curvature in further calculations via the surface or interface tracking method. The paper contains the data for the practical application of developed NNs. The method is limited to regular square or cuboid lattices.

Originality value

The paper presents an original implementation of NNs for normal vector calculation connected with CFD, LBM and other application for fluid flow with free surface or phase transformation.