bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotator: A Workbench for Sequence Annotation
Authors: Harris Nomi L.
Published: May 2017

Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signals such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching.

[Further details for obtaining Genotator are available at http://www.cshl.org/gr.]
A 3-Mb Contig from D11S987 to MLK3, a Gene-Rich Region in 11q13: Figure 1.
Authors: Smith Carissa M. , Ma Nancy S. , Nowak Norma J. , Shows Thomas B. , Gerhard Daniela S.
Published: May 2017

We have combined genetic, radiation-reduced somatic cell hybrid (RRH), fluorescent in situ hybridization (FISH), and physical mapping methods to generate a contig of overlapping YAC, PAC, and cosmid clones corresponding to >3 continuous Mb in 11q13. A total of 15 STSs [7 genes (GSTP1, ACTN, PC, MLK3, FRA1, SEA, HNP36), 4 polymorphic loci (D11S807, D11S987, GSTP1, D11S913), 3 ESTs (D11S1956E, D11S951E, and WI-12191), and 1 anonymous STS (D11S703)], mapping to three independent RRH segregation groups, identified 26 YAC, 7 PAC, and 16 cosmid clones from the CGM, Roswell Park, CEPH Mark I, and CEPH MegaYAC YAC libraries, a 5 genome equivalent PAC library, and a chromosome 11-specific cosmid library. Thirty-six Alu–PCR products derived from 10 anonymous bacteriophage λ clones, a cosmid containing the polymorphic markerD11S460, or STS-positive YAC or cosmid clones were identified and used to screen selected libraries by hybridization, resulting in the identification of 19 additional clones. The integrity and relative position of a subset of clones was confirmed by FISH and were found to be consistent with the physical and RRH mapping results. The combination of STS and Alu–PCR-based approaches has proven to be successful in attaining contiguous cloned coverage in this very GC-rich region, thereby establishing for the first time the absolute order and distance between the markers: CEN–MLK3–(D11S1956E/D11S951E/WI-12191)–FRA1–D11S460–SEA–HNP36/D11S913–ACTN–PCD11S703–GSTP1–D11S987–TEL.

[On-line supplementary material concerning screening materials and clones referred to in the text as Table 1 is available athttp://genome.wustl.edu/gerhard/gerhard.html or http://www.cshl.org/gr. The sequence data described in this paper have been submitted to the GenBank data library under accession no. AF009361.]
Mutations in myostatin (GDF8) in Double-Muscled Belgian Blue and Piedmontese Cattle
Authors: Kambadur Ravi , Sharma Mridula , Smith Timothy P.L. , Bass John J.
Published: May 2017

A visibly distinct muscular hypertrophy (mh), commonly known as double muscling, occurs with high frequency in the Belgian Blue and Piedmontese cattle breeds. The autosomal recessive mh locus causing double-muscling condition in these cattle maps to bovine chromosome 2 within the same interval as myostatin, a member of the TGF-β superfamily of genes. Because targeted disruption ofmyostatin in mice results in a muscular phenotype very similar to that seen in double-muscled cattle, we have evaluated this gene as a candidate gene for double-muscling condition by cloning the bovine myostatin cDNA and examining the expression pattern and sequence of the gene in normal and double-muscled cattle. The analysis demonstrates that the levels and timing of expression do not appear to differ between Belgian Blue and normal animals, as both classes show expression initiating during fetal development and being maintained in adult muscle. Moreover, sequence analysis reveals mutations in heavy-muscled cattle of both breeds. Belgian Blue cattle are homozygous for an 11-bp deletion in the coding region that is not detected in cDNA of any normal animals examined. This deletion results in a frame-shift mutation that removes the portion of the Myostatin protein that is most highly conserved among TGF-β family members and that is the portion targeted for disruption in the mouse study. Piedmontese animals tested have a G–A transition in the same region that changes a cysteine residue to a tyrosine. This mutation alters one of the residues that are hallmarks of the TGF-β family and are highly conserved during evolution and among members of the gene family. It therefore appears likely that the mh allele in these breeds involves mutation within the myostatin gene and that myostatin is a negative regulator of muscle growth in cattle as well as mice.

[The sequence data for bovine myostatin has been submitted to GenBank under accession no. AF019761.]
Characterization of Short Tandem Repeats from Thirty-One Human Telomeres
Authors: Rosenberg Marjorie , Hui Lester , Ma Junli , Nusbaum Harris C. , Clark Kevin , Robinson Louise , Dziadzio Laura , Swain Pamela M. , Keith Tim , Hudson Thomas J. , Biesecker Leslie G. , Flint Jonathan
Published: May 2017

Completion of genetic and physical maps requires markers from the ends (telomeres) of every human chromosome. We have searched for short tandem repeats (microsatellites) in cosmid and P1 clones and generated 661 sequence-tagged sites (STS) from the terminal 300 kb of 31 human chromosome ends. PCR assays were successfully designed for 58 microsatellites and mapped both genetically and on radiation hybrids (RHs) to confirm their telomeric location. Sequence analysis revealed marked variation in sequence composition, consistent with the hypothesis that even very highly GC-rich chromosome bands (the T bands) are not homogenous. The STSs that we have generated will be a necessary resource for the construction of physical maps of these complex regions of the genome.

[Information about the microsatellites is available electronically athttp://www.cshl.org/grand sequence has been deposited in the Genome Database (GDB).]
Cloning, Characterization, and Mapping of a Murine Promiscuous Chemokine Receptor Gene: Homolog of the Human Duffy Gene
Authors: Luo Hong , Chaudhuri Asok , Johnson Kenneth R. , Neote Kuldeep , Zbrzezna Valerie , He Yu , Pogo A. Oscar
Published: May 2017

We report here the isolation and genomic organization of the orthologous mouse Duffy gene, named Dfy. It is a single copy gene located in chromosome 1 in a region homologous to the human Duffy gene (FY). Sequence analyses indicate that Dfyconsists of two exons: exon 1 of 55 nucleotides, which encodes 7 amino acid residues; and exon 2 of 1038 nucleotides, which encodes 327 residues. The single intron consists of 462 nucleotides. The 5′-end promoter region contains motifs involved in vertebrate development in addition to potential binding sites of factors for globin transcription. The open reading frame (ORF) shows 60% homology with the human Duffy protein. However, mouse erythrocytes are serologically Duffy-negative and mouse erythrocyte membrane proteins do not cross-react with two Duffy-specific rabbit polyclonal antibodies. The deduced protein predicts a Mr of 36,692 and carries three potential N-glycosylation sites to asparagine residues. Hydropathy analysis predicts an exocellular amino-terminal domain of 57 residues, seven transmembrane α-helices, and an endocellular carboxy-terminal domain of 29 residues. In bone marrow and spleen,Dfy expresses a major 1.4-kb and a minor 1.8-kb mRNA. Contrary to humans, Dfy is expressed in liver, synthesizing a 1.4-kb mRNA, and is repressed in kidney. Dfy is highly expressed in mouse brain and produces a major 8.5-kb and a minor 10.2-kb mRNA. The human erythroleukemia K562 cells, transfected with cDNA encoding the mouse Duffy-like protein and mouse erythrocytes, have the same chemokine binding profiles indicating that they contain the same protein.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AF016584 and AF016697.]
Contig Maps and Genomic Sequencing Identify Candidate Genes in the Usher 1C Locus
Authors: Higgins Michael J. , Day Colleen D. , Smilinich Nancy J. , Ni L. , Cooper Paul R. , Nowak Norma J. , Davies Chris , de Jong Pieter J. , Hejtmancik Fielding , Evans Glen A. , Smith Richard J.H. , Shows Thomas B.
Published: May 2017

Usher syndrome 1C (USH1C) is a congenital condition manifesting profound hearing loss, the absence of vestibular function, and eventual retinal degeneration. The USH1C locus has been mapped genetically to a 2- to 3-cM interval in 11p14–15.1 between D11S899 andD11S861. In an effort to identify the USH1C disease gene we have isolated the region between these markers in yeast artificial chromosomes (YACs) using a combination of STS content mapping andAlu–PCR hybridization. The YAC contig is ∼3.5 Mb and has located several other loci within this interval, resulting in the orderCEN-LDHA-SAA1-TPH-D11S1310-(D11S1888/KCNC1)-MYOD1-D11S902D11S921-D11S1890-TEL.Subsequent haplotyping and homozygosity analysis refined the location of the disease gene to a 400-kb interval between D11S902 andD11S1890 with all affected individuals being homozygous for the internal marker D11S921. To facilitate gene identification, the critical region has been converted into P1 artificial chromosome (PAC) clones using sequence-tagged sites (STSs) mapped to the YAC contig, Alu–PCR products generated from the YACs, and PAC end probes. A contig of >50 PAC clones has been assembled between D11S1310 and D11S1890, confirming the order of markers used in haplotyping. Three PAC clones representing nearly two-thirds of the USH1C critical region have been sequenced. PowerBLAST analysis identified six clusters of expressed sequence tags (ESTs), two known genes (BIR,SUR1) mapped previously to this region, and a previously characterized but unmapped gene NEFA(DNA binding/EF hand/acidic amino-acid-rich). GRAIL analysis identified 11 CpG islands and 73 exons of excellent quality. These data allowed the construction of a transcription map for the USH1C critical region, consisting of three known genes and six or more novel transcripts. Based on their map location, these loci represent candidate disease loci for USH1C. The NEFA gene was assessed as the USH1C locus by the sequencing of an amplified NEFA cDNA from an USH1C patient; however, no mutations were detected.

[The sequence data described in this paper have been submitted to GenBank under accession numbersAC000406–AC000407.]
Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily
Authors: Leonard Christopher J. , Aravind L. , Koonin Eugene V.
Published: May 2017

The central role of serine/threonine and tyrosine protein kinases in signal transduction and cellular regulation in eukaryotes is well established and widely documented. Considerably less is known about the prevalence and role of these protein kinases in bacteria and archaea. In order to examine the evolutionary origins of the eukaryotic-type protein kinase (ePK) superfamily, we conducted an extensive analysis of the proteins encoded by the completely sequenced bacterial and archaeal genomes. We detected five distinct families of known and predicted putative protein kinases with representatives in bacteria and archaea that share a common ancestry with the eukaryotic protein kinases. Four of these protein families have not been identified previously as protein kinases. From the phylogenetic distribution of these families, we infer the existence of an ancestral protein kinase(s) prior to the divergence of eukaryotes, bacteria, and archaea.
Quality Assessment of Whole Genome Mapping Data in the Refined Familial Spastic Paraplegia Interval on Chromosome 14q
Authors: Paternotte Caroline , Rudnicki Doda , Fizames Cécile , Davoine Claire-Sophie , Mavel Delphine , Dürr Alexandra , Samson Delphine , Marquette Catherine , Muselet Delphine , Vega-Czarny Nathalie , Drouot Nathalie , Voit Thomas , Fontaine Bertrand , Gyapay Gabor , Auburger Georg , Weissenbach Jean , Hazan Jamilé
Published: May 2017

Autosomal dominant familial spastic paraplegia (AD-FSP) is a genetically heterogeneous neurodegenerative disorder characterized by progressive spasticity of the lower limbs. Three loci on chromosome 14q (SPG3), 2p (SPG4), and 15q (SPG6) were shown to be responsible for AD-FSP. Analysis of recombination events in three SPG3-linked families allowed us to narrow the critical interval from 9 to 5 cM. An ∼5-Mb YAC contig comprising 32 clones and 90 STSs was built from D14S301 to D14S991, encompassing this region of 14q21. Fifty-six ESTs assigned previously to this region with radiation hybrid (RH) panels Genebridge 4 and G3 were precisely localized on the YAC contig. The 90 STSs positioned on the contig were tested on the TNG RH panel to compare our YAC-based map with an RH map at a high level of resolution. Comparison between our map and the whole genome mapping data on this interval of chromosome 14q is discussed.
Homologs of the Yeast Longevity Gene LAG1 in Caenorhabditis elegans and Human
Authors: Jiang James C. , Kirchman Paul A. , Zagulski Marek , Hunt Jay , Jazwinski S. Michal
Published: May 2017

LAG1 is a longevity gene, the first such gene to be identified and cloned from the yeast Saccharomyces cerevisiae. A close homolog of this gene, which we call LAC1, has been found in the yeast genome. We have cloned the human homolog ofLAG1 with the ultimate goal of examining its possible function in human aging. In the process, we have also cloned a homolog from the nematode worm Caenorhabditis elegans. Both of these homologs,LAG1Hs and LAG1Ce-1, functionally complemented the lethality of a lag1Δ lac1Δdouble deletion, despite low overall sequence similarity to the yeast proteins. The proteins shared a short sequence, the Lag1 motif, and a similar transmembrane domain profile. Another, more distant human homolog, TRAM, which lacks this motif, did not complement.LAG1Hs also restored the life span of the double deletion, demonstrating that it functions in establishing the longevity phenotype in yeast. LAG1Hs mapped to 19p12, and it was expressed in only three tissues: brain, skeletal muscle, and testis. This gene possesses a trinucleotide (CTG) repeat within exon 1. This and its expression profile raise the possibility that it may be involved in neurodegenerative disease. This possibility suggests at least one way in which LAG1Hs might be involved in human aging.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AF105005–AF105009(LAG1Hs) and AF105010 (LAG1Ce-1).]
The Relative Power of Family-Based and Case-Control Designs for Linkage Disequilibrium Studies of Complex Human Diseases I. DNA Pooling
Authors: Risch Neil , Teng Jun
Published: May 2017

We consider statistics for analyzing a variety of family-based and nonfamily-based designs for detecting linkage disequilibrium of a marker with a disease susceptibility locus. These designs include sibships with parents, sibships without parents, and use of unrelated controls. We also provide formulas for and evaluate the relative power of different study designs using these statistics. In this first paper in the series, we derive statistical tests based on data derived from DNA pooling experiments and describe their characteristics. Although designs based on affected and unaffected sibs without parents are usually robust to population stratification, they suffer a loss of power compared with designs using parents or unrelateds as controls. Although increasing the number of unaffected sibs improves power, the increase is generally not substantial. Designs including sibships with multiple affected sibs are typically the most powerful, with any of these control groups, when the disease allele frequency is low. When the allele frequency is high, however, designs with unaffected sibs as controls do not retain this advantage. In designs with parents, having an affected parent has little impact on the power, except for rare dominant alleles, where the power is increased compared with families with no affected parents. Finally, we also demonstrate that for sibships with parents, only the parents require individual genotyping to derive the TDT statistic, whereas all the offspring can be pooled. This can potentially lead to considerable savings in genotyping, especially for multiplex sibships. The formulas and tables we derive should provide some guidance to investigators designing nuclear family-based linkage disequilibrium studies for complex diseases.
Modification of Bacterial Artificial Chromosome Clones Using Cre Recombinase: Introduction of Selectable Markers for Expression in Eukaryotic Cells
Authors: Kim Su Young , Horrigan Stephen K. , Altenhofen Janine L. , Arbieva Zarema H. , Hoffman Ronald , Westbrook Carol A.
Published: May 2017

Bacterial artificial chromosome clones (BACs) are widely used at present in human genome physical mapping projects. To extend the utility of these clones for functional genomic studies, we have devised a method to modify BACs using Cre recombinase to introduce a gene cassette into the loxP sequence, which is present in the vector portion of the BAC clone. Cre-mediated integration is site specific and thus maintains the integrity of the genomic insert sequences, while eliminating the steps that are involved in restriction digest-based DNA cloning strategies. The success of this method depends on the use of a DNA construct, RETRObac, which contains the reporter marker green fluorescent protein (GFP) and the selectable marker neomycin phosphotransferase (neo), but does not contain a bacterial origin of replication. BAC clones have been modified successfully using this method and the genomic insert shows no signs of deletions or rearrangements. Transfection efficiencies of the modified BACs into human or murine cell lines ranged from 1% to 6%. After culture in media containing G418 for 3 weeks, ∼0.1% of cells previously sorted for GFP expression acquired stable antibiotic resistance. Introduction of a human BAC clone that contains genomicp53 sequences into murine NIH3T3 cells led to expression of human p53 mRNA as determined by RT–PCR, demonstrating that sequences contained on the BAC are expressed. We believe that GFP–neo modified BAC clones will be a valuable resource in efforts to study biological effects of known genes as well as in efforts to clone and analyze new genes and regulatory regions.
A Pneumatic Device for Rapid Loading of DNA Sequencing Gels
Authors: Panussis Dimitrios A. , Cook Mark W. , Rifkin Lisa L. , Snider Jacqueline E. , Strong Joseph T. , McGrane Rebecca M. , Wilson Richard K. , Mardis Elaine R.
Published: May 2017

This work describes the design and construction of a device that facilitates the loading of DNA samples onto polyacrylamide gels for detection in the Perkin Elmer/Applied Biosystems (PE/ABI) 373 and 377 DNA sequencing instruments. The device is mounted onto the existing gel cassettes and makes the process of loading high-density gels less cumbersome while the associated time and errors are reduced. The principle of operation includes the simultaneous transfer of the entire batch of samples, in which a spring-loaded air cylinder generates positive pressure and flexible silica capillaries transfer the samples. A retractable capillary array carrier allows the delivery ends of the capillaries to be held up clear of the gel during loader attachment on the gel plates, while enabling their insertion in the gel wells once the device is securely mounted. Gel-loading devices capable of simultaneously transferring 72 samples onto the PE/ABI 373 and 377 are currently being used in our production sequencing groups while a 96-sample transfer prototype undergoes testing.
Rescue of Targeted Regions of Mammalian Chromosomes by in Vivo Recombination in Yeast
Authors: Kouprina Natalya , Kawamoto Kensaku , Barrett J. Carl , Larionov Vladimir , Koi Minoru
Published: May 2017

In contrast to other animal cell lines, the chicken pre-B cell lymphoma line, DT40, exhibits a high level of homologous recombination, which can be exploited to generate site-specific alterations in defined target genes or regions. In addition, the ability to generate human/chicken monochromosomal hybrids in the DT40 cell line opens a way for specific targeting of human genes. Here we describe a new strategy for direct isolation of a human chromosomal region that is based on targeting of the chromosome with a vector containing a yeast selectable marker, centromere, and an ARS element. This procedure allows rescue of the targeted region by transfection of total genomic DNA into yeast spheroplasts. Selection for the yeast marker results in isolation of chromosome sequences in the form of large circular yeast artificial chromosomes (YACs) up to 170 kb in size containing the targeted region. These YACs are generated by homologous recombination in yeast between common repeated sequences in the targeted chromosomal fragment. Alternatively, the targeted region can be rescued as a linear YACs when a YAC fragmentation vector is included in the yeast transformation mixture. Because the entire isolation procedure of the chromosomal region, once a target insertion is obtained, can be accomplished in ∼1 week, the new method greatly expands the utility of the homologous recombinationproficient DT40 chicken cell system.
Complex β-Satellite Repeat Structures and the Expansion of the Zinc Finger Gene Cluster in 19p12
Authors: Eichler Evan E. , Hoffman Susan M. , Adamson Aaron A. , Gordon Laurie A. , McCready Paula , Lamerdin Jane E. , Mohrenweiser Harvey W.
Published: May 2017

We investigated the organization, architecture, and evolution of the largest cluster (∼4 Mb) of Krüppel-associated box zinc finger (KRAB–ZNF) genes located in cytogenetic band interval 19p12. A highly integrated physical map (∼700 kb) of overlapping cosmid and BAC clones was developed between genetic STS markers D19S454 and D19S269. Using ZNF91 exon-specific probes to interrogate a detailed EcoRI restriction map of the region, ZNF genes were found to be distributed in a head-to-tail fashion throughout the region with an average density of one ZNF duplicon every 150–180 kb of genomic distance. Sequence analysis of 208,967 bp of this region indicated the presence of two putative ZNF genes: one consisting of a novel member of this gene family (ZNF208) expressed ubiquitously in all tissues examined and the other representing a nonprocessed pseudogene (ZNF209), located 450 kb proximal toZNF208. Large blocks of (∼25-kb) inverted β-satellite repeats with a remarkably symmetrical higher order repeat structure were found to bracket the functional ZNF gene. Hybridization analysis using the β-satellite repeat as a probe indicates that β-satellite interspersion between ZNF gene cassettes is a general property for 1.5 Mb of the ZNF gene cluster in 19p12. Both molecular clock data as well as a retroposon-mapping molecular fossil approach indicate that this ZNF cluster arose early during primate evolution (∼50 million years ago). We propose an evolutionary model in which heteromorphic pericentromeric repeat structures such as the β satellites have been coopted to accommodate rapid expansion of a large gene family over a short period of evolutionary time.

[The sequence data described in this paper have been submitted to GenBank under accession nos. AC003973 and AC004004.]
Molecular Basis for the Dominant White Phenotype in the Domestic Pig
Authors: Marklund Stefan , Kijas James , Rodriguez-Martinez Heriberto , Rönnstrand Lars , Funa Keiko , Moller Maria , Lange Dirk , Edfors-Lilja Inger , Andersson Leif
Published: May 2017

The change of phenotypic traits in domestic animals and crops as a response to selective breeding mimics the much slower evolutionary change in natural populations. Here, we describe that the dominant white phenotype in domestic pigs is caused by two mutations in theKITgene encoding the mast/stem cell growth factor receptor (MGF), one gene duplication associated with a partially dominant phenotype and a splice mutation in one of the copies leading to the fully dominant allele. The splice mutation is a G to A substitution in the first nucleotide of intron 17 and leads to skipping of exon 17. The duplication is most likely a regulatory mutation affecting KIT expression, whereas the splice mutation is expected to cause a receptor with impaired or absent tyrosine kinase activity. Immunocytochemistry showed that this variant form is expressed in 17- to 19-day-old pig embryos. Hundreds of millions of white pigs around the world are assumed to be heterozygous or homozygous for the two mutations.

[The EMBL accession numbers for porcineKIT1*0101, KIT1*0202, KIT2*0202,andKIT2*0101areAJ223228–AJ223231, respectively.]
Direct Selection of Conserved cDNAs from the DiGeorge Critical Region: Isolation of a Novel CDC45-Like Gene
Authors: McKie Judith M. , Wadey Roy B. , Sutherland Helen F. , Taylor Catherine L. , Scambler Peter J.
Published: May 2017

We have used a modified direct selection technique to detect transcripts that are both evolutionary conserved and developmentally expressed. The enrichment for homologous mouse cDNAs by use of human genomic DNA as template is shown to be an efficient and rapid approach for generating transcript maps. Deletions of human 22q11 are associated with several clinical syndromes, with overlapping phenotypes, for example, velocardiofacial syndrome (VCFS) and DiGeorge syndrome (DGS). A large number of transcriptional units exist within the defined critical region, many of which have been identified previously by direct selection. However, no single obvious candidate gene for the VCFS/DGS phenotype has yet been found. Our technique has been applied to the DiGeorge critical region and has resulted in the isolation of a novel candidate gene, Cdc45l2, similar to yeast Cdc45p.

[The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AJ0223728 and AF0223729.]
Sequencing of cDNA Clones from the Genetic Map of Tomato (Lycopersicon esculentum)
Authors: Ganal Martin W. , Czihal Rosemarie , Hannappel Ulrich , Kloos Dorothee-U. , Polley Andreas , Ling Hong-Qing
Published: May 2017

The dense RFLP linkage map of tomato (Lycopersicon esculentum) contains >300 anonymous cDNA clones. Of those clones, 272 were partially or completely sequenced. The sequences were compared at the DNA and protein level to known genes in databases. For 57% of the clones, a significant match to previously described genes was found. The information will permit the conversion of those markers to STS markers and allow their use in PCR-based mapping experiments. Furthermore, it will facilitate the comparative mapping of genes across distantly related plant species by direct comparison of DNA sequences and map positions.

[cDNA sequence data reported in this paper have been submitted to the EMBL database under accession nos.AA824695–AA825005 and the dbEST_Id database under accession nos. 1546519–1546862.]
The most influential researchers in information behaviour
Authors: Soheili Faramarz , Khasseh Ali Akbar , Mousavi-Chelak Afshin
Published: May 2017

Purpose

The purpose of this paper is to identify the top researchers in information behaviour (IB) based on ideational and social influence indicators.

Design/methodology/approach

The population included papers on IB indexed in the Web of Science from 1980 to 2015. UCINET and Bibexcel were the tools used for measuring the ideational and social influence indicators. The correlations among the study variables were measured by applying SPSS and LISREL.

Findings

There was a significant relationship between IB researchers’ productivity and performance, and between ideational influence and social influence. The structural equation modelling showed that a researcher with top placement in his/her co-authorship network can gain higher ideational influence. In total, it seems that the single and traditional criteria are increasingly replacing new and integrative ones in measuring researchers’ scientific influence in fields including IB studies. Results have shown that based on total scores of the studied indicators, Spink, A., Nicholas, D., Ford, N., Huntington, P., Wilson, T.D., and Jamali, H.R. gained the high scores.

Originality/value

The current study used an integrative method based on influence indicators to identify the influential researchers in IB studies. None of the few studies done using bibliometric methods in the realm of IB has investigated the ideational and social influence indicators altogether.
Are Mendeley reader counts high enough for research evaluations when articles are published?
Authors: Thelwall Mike
Published: May 2017

Purpose

Mendeley reader counts have been proposed as early indicators for the impact of academic publications. The purpose of this paper is to assess whether there are enough Mendeley readers for research evaluation purposes during the month when an article is first published.

Design/methodology/approach

Average Mendeley reader counts were compared to the average Scopus citation counts for 104,520 articles from ten disciplines during the second half of 2016.

Findings

Articles attracted, on average, between 0.1 and 0.8 Mendeley readers per article in the month in which they first appeared in Scopus. This is about ten times more than the average Scopus citation count.

Research limitations/implications

Other disciplines may use Mendeley more or less than the ten investigated here. The results are dependent on Scopus’s indexing practices, and Mendeley reader counts can be manipulated and have national and seniority biases.

Practical implications

Mendeley reader counts during the month of publication are more powerful than Scopus citations for comparing the average impacts of groups of documents but are not high enough to differentiate between the impacts of typical individual articles.

Originality/value

This is the first multi-disciplinary and systematic analysis of Mendeley reader counts from the publication month of an article.
Disruptive innovation in rural American healthcare: the physician assistant practice
Authors: Kushins Eric R. , Heard Henry , Weber J. Michael
Published: May 2017

Purpose

This article proposes a new disruptive innovation in healthcare through the development of a physician assistant business model, which can be most readily applied in vulnerable rural health care settings.

Design/methodology/approach

This study reviews the current state of the health care system in terms of physician assistant utilization and primary care shortages in rural communities. The study proposes that the physician assistant-owned and -operated primary care business represents a disruptive innovation, via the application of the five principles of Clayton Christensen’s (1997) thesis on disruptive innovation.

Findings

Considering the current state of the health care industry, the study logically defends the proposed model as a disruptive innovation in that it: focuses on an underserved market, has lower costs, has few competitors, offers high quality and provides a sustainable competitive advantage.

Practical implications

The physician assistant business model is a viable solution for providing primary care for rural communities with educational, financial, transportation and other resource limitations.

Originality/value

This is a unique application of the theory of disruptive innovation, which illustrates how a new business model can solve a chronic shortage in primary care, especially in underserved populations.
Listening to Immokalee moms
Authors: Morton Cynthia , Galindo Sebastian , Morera Maria , Dodoo Naa , Gonzalez Cristobal , Wu Linwan , Fundingsland Suzanne , Auguste Kendra , Headrick Lauren , Monaghan Paul , Shelnutt Karla
Published: May 2017

Purpose

The purpose of this paper is to present a case study of the research steps taken to identify message directions for a community-wide health communication campaign aimed at supporting healthier eating behaviors among Latino farmworker families in the Immokalee community in Florida. Latino mothers were targeted to understand their beliefs about children’s healthy eating needs and identify communication campaign opportunities that would reinforce choices made in the home, surrounding meal planning, food selection and preparation and portion sizes.

Design/methodology/approach

A sequential mixed-methods approach using focus group, group interview and qualitative message concept testing was used in three distinct stages of research exploration. An independent sample was recruited at each stage through convenience sampling and snowball sampling methods. The stages of change theory provided a framework for research inquiry in the context of healthy eating-at-home practices.

Findings

In general, mothers were aware and participatory in the effort to serve healthy meals for their children at home. The time and money associated with buying nutritious foods and cooking healthy meals daily was stressful, but they were receptive to communication efforts to help them maintain their commitment to give their children healthy foods. These findings provided directional opportunities for the discovery and implementation of health communication strategies. Test results found that the target was most receptive to message strategies that acknowledged the responsibility of both parents to model healthy eating practices to children.

Research limitations/implications

Recruiting resulted in small sample sizes at each stage of the investigation. The reliability of quantitative measurement was a limitation to the research conclusions.

Practical implications

Partnership with the audience from discovery to conceptualization resulted in messages that uniquely resonated with the audience for which they were aimed. Understanding about the target stage of readiness improves message effectiveness to the target group.

Social implications

Health communication campaigns planned and developed with the target audience at its center will generate message strategies that effectively address issues of greatest relevance to those communication agents that seek to change.

Originality/value

The study provides a unique exploration of the steps that health communication agents should pursue to establish a thorough profile of their target audience and the issues that resonate when considering healthy eating behavior at home. The application of the stages of the change model encouraged the discovery of issues surrounding the challenge and highlighted potential obstacles that would mitigate the behavior change efforts.
Influence of the thickness of intumescent paint in the position of steels (fire safety)
Authors: Garcia Harkaitz , Biezma María Victoria , Cuadrado Jesús , Rojí Eduardo
Published: May 2017

Purpose

The purpose of this paper is to analyze a new structural design applied in industrial frames using two type of steels (S275 and fire resistant (FR)) with different mechanical resistance against fire. To do it, the authors have taken into account variables such as intrinsic metallic design, span length, intumescent paint thickness, and fire time exposure, which offers information about new scenarios of design in industry.

Design/methodology/approach

The key methodology followed has taken into account a modeling program that uses the following variables: 25 and 35 m of span, 45 and 60 fire exposure times, and seven different intumescent paint thickness. An optimum structural design has been evaluated by discretization of each scenario with the particular type of steel, S275 and FR. The obtained approach could be a good guideline for future designs.

Findings

The results and analysis have shown a very good and valid idea of a new structural typology using optimum intumescent paint thickness into the final design of the industrial frame considering that it has two different types of steel. It is in realty a handicap since usually mechanical engineers employ structural steel without paying attention to this new feature.

Practical implications

Cheaper structural designs could be obtained using the two different types of steel considering the proper positioning into the full building.

Originality/value

The validity of design of two types of steel plus intumescent paint in building construction has been shown, and this study will encourage designers to use it, in particular in buildings with high fire risk.
Pushing similarity joins down to the storage layer in XML databases
Authors: Andrade Ribeiro Leonardo , Härder Theo
Published: May 2017

Purpose

This article aims to explore how to incorporate similarity joins into XML database management systems (XDBMSs). The authors aim to provide seamless and efficient integration of similarity joins on tree-structured data into an XDBMS architecture.

Design/methodology/approach

The authors exploit XDBMS-specific features to efficiently generate XML tree representations for similarity matching. In particular, the authors push down a large part of the structural similarity evaluation close to the storage layer.

Findings

Empirical experiments were conducted to measure and compare accuracy, performance and scalability of the tree similarity join using different similarity functions and on the top of different storage models. The results show that the authors’ proposal delivers performance and scalability without hurting the accuracy.

Originality/value

Similarity join is a fundamental operation for data integration. Unfortunately, none of the XDBMS architectures proposed so far provides an efficient support for this operation. Evaluating similarity joins on XML is challenging, because it requires similarity matching on the text and structure. In this work, the authors integrate similarity joins into an XDBMS. To the best of the authors’ knowledge, this work is the first to leverage the storage scheme of an XDBMS to support XML similarity join processing.
Tribological properties of Fe-Cr-B alloy for sliding boot in coal mining machine under dry sliding condition
Authors: Xuan Hongbin , Cui Gongjun
Published: May 2017

Purpose

To improve the wear resistance of the sliding boot, the wear-resistant Fe-21 Wt.% Cr-5 Wt.% B alloy is prepared, and the wear mechanism is studied under dry sliding condition.

Design/methodology/approach

The anti-wear Fe-21 Wt.% Cr-5 Wt.% B alloy is prepared by powder metallurgy technique. The tribological behavior of Fe-Cr-B alloy sliding against ASTM 1045 steel pin is studied at 30-60 N and 0.03-0.12 m/s using a reciprocating pin-on-disk tribometer under dry sliding condition. Meanwhile, the ASTM 5140 and 3316 steel are studied as compared samples.

Findings

The friction coefficients of tested specimens increase with the increasing normal load. However, this effect is the opposite in case of different sliding speeds. The specific wear rates increase as the sliding speed and normal load increase. The Fe-Cr-B alloy shows the best tribological properties under the dry sliding condition and the wear mechanism is mainly ploughing.

Originality/value

This wear-resistant Fe-21 Wt.% Cr-5 Wt.% B alloy can replace the traditional materials to process the sliding shoes and improve the service life of coal mining machine.
Student perceptions of relevance in a research methods course
Authors: Owen Leanne
Published: May 2017

Purpose

The purpose of this paper is to demonstrate that a deliberate effort to link course content to students’ personal or professional goals results in increased student perceptions of relevance.

Design/methodology/approach

Self-report data were collected using questionnaires that were administered to students in a research methods course over a period of three semesters. Results were compared in order to determine whether the introduction of guest speakers, hands-on activities, and pertinent video clips fostered greater perceptions of relevance in specific learning units.

Findings

Although there was some variation, data revealed that students reported the greatest increases in their perceptions of specific course content as relevant if that content was explicitly and clearly linked to a potentially practical professional application.

Research limitations/implications

The sample size was inconsistent and self-report studies may be viewed as unreliable. The instrument used may benefit from the inclusion of concrete behavioral frequency statements.

Practical implications

If faculty members can make explicit connections and persuade students’ perceptions of the relevance of course content, students may develop greater motivation to learn, a deeper understanding of the material, and a propensity for long-term transfer.

Originality/value

Although a number of studies have investigated the causal link between perceived relevance of course content and the attainment of academic or professional goals, none have tracked changes in student perceptions of relevance as a direct result of deliberate faculty efforts to make the relevance of course content explicitly clear for students.
The influence of foreign investment on Malaysian Bumiputera technology firms: 1957-2016
Authors: Abdul Kohar Umar Haiyat , McMurray Adela J. , Peszynski Konrad
Published: May 2017

Purpose

The purpose of this paper is to identify the historical influences and chronological development of foreign investors on Malaysian Bumiputera (indigenous) new technology-based small firms (NTBSFs).

Design/methodology/approach

Weick’s (1989) conceptual theory building approach is used to conduct a critical historical documentary analysis of the international, local, academic and government inward foreign investments literature from prior Malaysia’s independence (1957) through to 2016.

Findings

Increased foreign investment between 1957 and 2016 proved to be effective for Malaysia to transform its economy from a reliance on primary production to a focus on innovation and value-added industries such as the biotechnology and the information and communication and technology sectors.

Research limitations/implications

Local and international literature addressing inward foreign investments towards host countries yielded four key research implications: employment effects, strategic alliances, technology transfer and knowledge transfer. Creation of firm-specific resources in addition to government assistance, particularly through grants and advisory services, significantly contribute to the sustainability of Bumiputera NTBSFs.

Practical implications

Inward foreign investment through subsidiary multi-national companies (MNCs) leads to the formation of strategic alliances between MNCs and Bumiputera NTBSFs, generating employment opportunities, contributing to Malaysia’s development aims.

Social implications

Charting the chronological development and historical influence of foreign investment from a Malay-Bumiputera perspective provides an in-depth understanding of the evolution of what is now a multi-cultural Malaysian society.

Originality/value

This study provides a chronological development and discussion of the historical influences and implications of foreign investment towards the evolution and sustainability of Malaysian Bumiputera NTBSFs.
Employee empowerment and its contextual determinants and outcome for service workers
Authors: Kim Peter Beomcheol , Lee Gyumin , Jang Jichul
Published: May 2017

Purpose

The purpose of this paper is to investigate a research model of employee empowerment along with its contextual determinants (i.e. leader-member exchange (LMX) and schedule flexibility) and primary consequence (i.e. service performance) for restaurant workers in New Zealand and South Korea. The study further examines a moderating role of national differences derived from the power distance theory for the hypothesized paths between empowerment and its determinants and consequences.

Design/methodology/approach

This study utilized traditional paper-and-pencil surveys for data collection. A final sample of 303 service employees from restaurants in New Zealand (n=152) and South Korea (n=151) was used to test research hypotheses by structural equation modeling using LISREL (version 8.80).

Findings

The study concludes with two core findings supporting research hypotheses. First, as hypothesized, employees who consider their schedule flexible with high LMX quality with their immediate supervisor are more likely to feel empowered, and empowered workers are more likely to perform well in customer services. Furthermore, the results show that the impact of schedule flexibility and LMX on empowerment and the impact of empowerment on service performance are more salient among South Korean employees than their New Zealand counterpart.

Originality/value

Based on job characteristics, work adjustment, and social exchange theories, this study develops and tests a research model of employee empowerment including service context-relevant determinants, i.e., schedule flexibility and LMX, as well as a crucial work outcome, i.e., service performance, using two different national samples. The findings of this study contribute to the body of knowledge in understanding the organizational dynamic of employee empowerment in the service industry, suggesting that managers incorporate relevant contextual practices to promote empowerment, which ultimately enhances employees’ service performance. It is also recommended that such practices are carefully implemented, taking into consideration the cultural background of the workforce.
Operational efficiency of ASEAN airlines: based on DEA and bootstrapping approaches
Authors: Hu Jin-Li , Li Yang , Tung Hsin-Jing
Published: May 2017

Purpose

For strategic and competitive insights, the purpose of this paper is to measure and benchmark the comparative operating efficiencies of Association of Southeast Asian Nations’ (ASEAN) major airlines and present a new interpretation along with managerial implications.

Design/methodology/approach

This research statistically tests returns to scale and the equality of mean efficiencies for 15 ASEAN airlines covering the period 2010-2014. The disaggregate input efficiency of ASEAN airlines is computed by comparing the target and actual inputs.

Findings

The disaggregate input efficiency of ASEAN airlines shows that aircraft efficiency is the lowest, operating cost efficiency is better, and available seat efficiency is the best.

Originality/value

This paper applies data envelopment analysis models, disaggregated input efficiency measures, and bootstrapping approaches to compute the operational efficiency of ASEAN airlines. Strategic suggestions are made to improve the operational efficiency of ASEAN airlines.