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Analysis of the structure of original research papers: an aid to writing original papers for publication.

BACKGROUND: An increasing number of people involved in medicine are under pressure to publish research, but there is little understanding of how to describe structured writing. AIM: This paper aims to describe the structure of original research papers published in the British Journal of General Practice with a view to providing insight into the nature of such analyses, and particularly to help researchers and trainers to write and teach writing more successfully. METHOD: A sample of 50 original papers published in the Journal between January 1989 and March 1993 were examined. The papers were subjected to a form of 'move structure analysis', a technique used in applied linguistics; move structure analysis assigns a tentative function to a piece of text, and identifies words/phrases associated with it. To be recognized, moves thus identified had to occur in the same section of the paper in 65% of the corpus, and/or appear in the same order relative to other moves in 50%. RESULTS: Fifteen moves were identified, four in the introduction, three in the method, and four each in the results and discussion. These moves functioned, for example in the discussion, to state limitations and defend successes; describe achievements; contextualize procedures and findings; and offer recommendations. Frequency scores ranged from 66% to 100%, and order stability scores from 50% to 80%, with three moves being unordered. CONCLUSION: It is possible to derive from this study a template for structuring academic medical writing. This template may be built up from the exemplary quotations in the text, to provide assistance to educators and less experienced writers.

Publishing↗

[Determination of various toxic minerals in spiruline algae of different origins, and evaluation of long-term toxicity in the rat of a lot of spiruline algae of Mexican origin].

A detailed analytical study made on samples of Spirulines algae of various origins showed that these microorganisms may present an important telluric contamination, especially demonstrated by high levels of fluorine and arsenic they contain. A long term animal experimentation has been achieved with Spirula Maxima, obtained from the Sosa Texcoco solar evaporator. A diet contained in total proteins 25 p. 100 of dried atomized algae and was given for 75 weeks to Wistar rats. All along the experiment, the animals submitted to that diet showed no difference with control animals fed with caseine. The increase in weight was comparable for control animals and male experimented animals; a slight decrease in weight has been observed for females fed with algae up to the 30th week. At the end of the experiment, a normal frequency of tumours was noted on experimented animals. The cumulative potentiality of certain mineral toxicants, has been evaluated, when abnormal high levels of them have been detected in the Spirulines samples. The fed animals have been killed at definite times all along the experiment and the metals dosed in the body. Such a cumulative potency has been demonstrated for arsenic. On the contrary, in the case of fluorine, even particular dosages in the femoral bone could not show any significant cumulation of that toxicant, comparing with control animals. In conclusion, the authors have not noted any evident toxicity related to the samples of Spirulines tested in rats, whatever these algae were the only source of proteins in the diet. They hope anyway that the exact origin of contamination of these algaes by these metals will be better known to prevent the variations in the composition of industrial samples of Spirulines according to these metals for instance.

Animals↗

[Double origin of anterior descending artery--from the left and right coronary arteries--associated with anomalous origin of the circumflex artery].

A 65 year-old white man, with typical angina pectoris, underwent coronary angiography that showed dual left anterior descending artery (LAD), originating from the right coronary artery (RCA), associated with anomalous origin of the left circumflex artery (LCX) also from the RCA. This an extremely rare coronary artery anomaly and, it is the first case reported, so far. This rareness and clinical significance are emphasized.

Aged↗

Origin of life: a hypothesis for the origin of adaptor-mediated ordered synthesis of proteins and an explanation for the choice of terminating codons in the genetic code.

Life can be defined as a system of self-sustained chemical processes springing from the ordered synthesis of proteins directed by nucleic acids. To the notoriously difficult problem of the origin of this basic process of nucleic acid-directed protein synthesis, we give a solution of molecular interactions between pentanucleotides and amino acids. A particular conformation of a pentanucleotide forms a double sided template, with its 'inside' capable of nestling an amino acid while the 'outside' acts as an adaptor to a 'codon' triplet on long-chain nucleic acids. This serves as a primitive decoding system. An important aspect of our postulate is that a dynamic interaction is triggered, by this decoding system, through which amino acids are brought to juxtaposition facilitating peptide bond formation. Almost all the important and unique features of contemporary protein-synthesizing machinery are seen to be a direct and natural consequence of our postulate. The emergence of the termination codons also fits in, as a natural consequence of this molecular mechanism.

Animals↗

Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function.

The minimal replicator of the Epstein-Barr virus (EBV) latent cycle origin of DNA replication oriP is composed of two binding sites for the Epstein-Barr virus nuclear antigen-1 (EBNA-1) and flanking inverted repeats that bind the telomere repeat binding factor TRF2. Although not required for minimal replicator activity, additional binding sites for EBNA-1 and TRF2 and one or more auxiliary elements located to the right of the EBNA-1/TRF2 sites are required for the efficient replication of oriP plasmids. Another region of oriP that is predicted to be destabilized by DNA supercoiling is shown here to be an important functional component of oriP. The ability of DNA fragments of unrelated sequence and possessing supercoiled-induced DNA duplex destabilized (SIDD) structures, but not fragments characterized by helically stable DNA, to substitute for this component of oriP demonstrates a role for the SIDD region in the initiation of oriP-plasmid DNA replication.

DNA Helicases↗

The chemistry in circumstellar envelopes of evolved stars: following the origin of the elements to the origin of life.

Mass loss from evolved stars results in the formation of unusual chemical laboratories: circumstellar envelopes. Such envelopes are found around carbon- and oxygen-rich asymptotic giant branch stars and red supergiants. As the gaseous material of the envelope flows from the star, the resulting temperature and density gradients create a complex chemical environment involving hot, thermodynamically controlled synthesis, molecule "freeze-out," shock-initiated reactions, and photochemistry governed by radical mechanisms. In the circumstellar envelope of the carbon-rich star IRC+10216, >50 different chemical compounds have been identified, including such exotic species as C(8)H, C(3)S, SiC(3), and AlNC. The chemistry here is dominated by molecules containing long carbon chains, silicon, and metals such as magnesium, sodium, and aluminum, which makes it quite distinct from that found in molecular clouds. The molecular composition of the oxygen-rich counterparts is not nearly as well explored, although recent studies of VY Canis Majoris have resulted in the identification of HCO(+), SO(2), and even NaCl in this object, suggesting chemical complexity here as well. As these envelopes evolve into planetary nebulae with a hot, exposed central star, synthesis of molecular ions becomes important, as indicated by studies of NGC 7027. Numerous species such as HCO(+), HCN, and CCH are found in old planetary nebulae such as the Helix. This "survivor" molecular material may be linked to the variety of compounds found recently in diffuse clouds. Organic molecules in dense interstellar clouds may ultimately be traced back to carbon-rich fragments originally formed in circumstellar shells.

Astronomical Phenomena↗

Circulating and ex vivo production of pyrogenic cytokines and interleukin-1 receptor antagonist in 123 patients with fever of unknown origin. The Netherlands Fever of Unknown Origin Study Group.

Circulating and ex vivo production of interleukin (IL)-1beta, tumor necrosis factor (TNF)-alpha, IL-6, and IL-1 receptor antagonist (ra) and the diagnostic utility of these cytokines were studied in 123 patients with fever of unknown origin (FUO). Diagnoses were infections, 28; neoplasms, 14; noninfectious inflammatory diseases (NIID), 32; miscellaneous diseases, 10; and none made, 39. IL-1beta, IL-6, and IL-1ra concentrations were higher in patients with infections, neoplasms, and NIID than in healthy controls. Patients with infections had higher concentrations of TNF-alpha than controls. The ex vivo production of IL-1beta and IL-1ra in all patients with FUO did not differ from that in controls; however, production of TNF-alpha was lower in patients with neoplasms and NIID, and IL-6 production was lower in patients with neoplasms. Thirty-five patients with fever did not have elevated cytokines. Although some significant differences were found among the diagnostic subgroups, there was wide variation. Thus, measurement of these cytokines does not aid in the diagnosis of FUO.

Adolescent↗

Management of children with prolonged fever of unknown origin and difficulties in the management of fever of unknown origin in children in developing countries.

This is Part II of a 2-part paper on fever of unknown origin (FUO) in children. It examines the aetiology and management of prolonged FUO in children and the difficulties in the management of FUO in children in developing countries. Part I of this paper discussed acute FUO in children and was published in the March 2001 issue of Paediatric Drugs. Prolonged FUO is documented fever of more than 7 to 10 days which has no apparent source and no apparent diagnosis after 1 week of clinical investigations. About 34% of cases of prolonged FUO are caused by infections, with bacterial meningitis and urinary tract infection accounting for about 6.5 and 11.4%, respectively, of cases attributable to infections. Chronic infections, particularly tuberculosis and 'old' disorders such as Kawasaki disease, cat-scratch disease and Epstein-Barr virus infection presenting with 'new' manifestations, collagen-vascular diseases and neoplastic disorders are the other issues of major concern in prolonged FUO. Overall, however, there is a trend towards an increased number of undiagnosed cases. This is due to advancements in diagnostic techniques, such that illnesses which were previously common among the causes of prolonged FUO are now diagnosed earlier, before the presentation becomes that of prolonged FUO. Clinical examination supplemented with laboratory tests to screen for serious bacterial infections should be the mainstay of initial evaluation of children with prolonged FUO. Use of scanning techniques (such as computerised tomography and ultrasound) as additional supplements to this clinical examination may allow for the earlier diagnosis of causes of prolonged FUO in children such as 'occult' abdominal tumours. A common error in management of children with prolonged FUO is the failure to perform a complete history and physical examination; repeated clinical examination and continued observation are of paramount importance in the diagnosis of difficult cases. Major difficulties in the management of FUO in children in developing countries include constraints in the availability and reliability of laboratory tests, cost, misuse of antibiotics and difficulties encountered in the diagnosis of malaria and typhoid fever. Malaria and typhoid fever are major aetiological considerations in both acute and prolonged FUO in children in developing countries. The newer quinolones may hold great promise for the treatment of serious bacterial infections, including meningitis, which are associated with prolonged FUO in developing countries.

Child↗

Compound heterozygous patient with glycogen storage disease type III: identification of two novel AGL mutations, a donor splice site mutation of Chinese origin and a 1-bp deletion of Japanese origin.

Glycogen storage disease type III (GSD III) is an autosomal recessive disorder caused by deficiency of glycogen-debranching enzyme (AGL). We studied a 2-year-old GSD III patient whose parents were from different ethnic groups. Nucleotide sequence analysis of the patient showed two novel mutations: a single cytosine deletion at nucleotide 2399 (2399delC) in exon 16, and a G-to-A transition at the +5 position at the donor splice site of intron 33 (IVS33+5G>A). Analysis of the mRNA produced by IVS33+5G>A showed aberrant splicing: skipping of exon 33 and activation of a cryptic splice site in exon 34. Mutational analysis of the family revealed that the 2399delC was inherited from her father, who is of Japanese origin, and the IVS33+5G>A from her mother, who is of Chinese descent, establishing that the patient was a compound heterozygote. To our knowledge, this is the first report of a mutation identified in a GSD III patient from the Chinese population.

Child, Preschool↗

A novel tRNA species as an origin of short interspersed repetitive elements (SINEs). Equine SINEs may have originated from tRNA(Ser).

Short interspersed repetitive elements (SINEs) were isolated from the equine genome and characterized. The equine SINE (ERE-1) family has several features characteristic of tRNA-derived retroposons. The five members of the equine family of SINEs are approximately 230 nucleotides in length and terminate with a sequence rich in oligo(A). They are all flanked by direct repeats at the 5' and 3' ends, and such repeats are the hallmarks of retroposons. In addition, the ERE-1 family has a tRNA-related region, which is similar to tRNA(Ser) of Drosophila (65% identity). tRNA(Ser) is a novel tRNA with respect to the origin of SINEs and has not previously been recognized among the twenty tRNA-derived SINEs characterized to date. The members of the ERE-1 family were found to be distributed among five species in the genus Equus, and their amplification may have contributed to the genetic variability of their hosts during evolution.

Animals↗

Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. I. Isolation and characterization of plasmids containing the origin region.

A BamHI restriction endonuclease fragment, B7, which is replicated first among all other fragments derived from the Bacillus subtilis chromosome, was cloned in Escherichia coli using as vector a hybrid plasmid pMS102 that can replicate both in E. coli and B. subtilis. Digestion of pMS102 with BamHI produced two fragments and the smaller one was replaced by the B7 fragment. The cloned plasmid pMS102'-B7 exhibited some peculiar properties that were not observed with plasmids containing other fragments from the B. subtilis chromosome. (1) E. coli cells harboring this plasmid stuck to each other and to glass. This property was more apparent when cells were grown in poor media. (2) E. coli cells tended to lose the plasmid spontaneously when they were grown without the selective pressure favorable to the plasmid. (3) The frequency of transformation of B. subtilis by pMS102'-B7 was less than 1/1,000 of that by the vector plasmid pMS102'. The number of copies of pMS102'-B7 present in the transformants was also markedly reduced, although the pUB110 origin of replication on the vector was intact and should be functional in B. subtilis. This inhibitory effect of the B7 fragment on plasmid replication was confirmed more directly by developing a semi in vitro replication system using protoplasts. Both in E. coli and B. subtilis the B7 fragment affected replication of its own molecule but not that of the coexisting plasmid with an identical replication system. The implication of the function of the B7 fragment in the initiation of the B. subtilis chromosome will be discussed.

Bacillus subtilis↗

Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. II. Identification of the essential regions for inhibitory functions shown by the DNA segment containing the replication origin.

A BamHI restriction endonuclease fragment B7, which contains the replication origin of the Bacillus subtilis chromosome, showed inhibitory effects on cell growth and plasmid replication in Escherichia coli and Bacillus subtilis, when B7 was inserted into a composite plasmid pMS102' and introduced into these cells. In order to localize these properties in more limited regions within the B7 fragment, we developed a new and widely applicable method for deletion of DNA segments of various lengths from one or other end of a given region of the plasmid molecule. Using a set of deletions in the B7 fragments of pMS102'-B7, we determined the loci responsible for the inhibitory effects of B7 as described below. (1) Stickiness appearing in E. coli cells was caused by a segment residing in a region of approximately 2.2 kilobase pairs (kbp) overlapping the E19 and E22 fragments. (2) instability of the plasmid in E. coli was due to a segment localized in the 440 bp region of the E19-side terminal portion of the 2.2 kbp region. (3) The same 440 bp were also responsible for inhibition of the replication of the plasmid in B. subtilis. Hybridization of the cloned DNA fragments containing the 2.2 kbp region with the whole B. subtilis chromosome revealed that several regions of the chromosome are homologous to this characteristic sequence.

Bacillus subtilis↗

Nuclear and chloroplast DNA reassessment of the origin of Indian potato varieties and its implications for the origin of the early European potato.

The modern cultivated potato was first recorded in Europe in 1562, but its area(s) of exportation has long been in dispute. Two competing hypotheses have proposed an "Andean" area (somewhere from upland Venezuela to northern Argentina) or a lowland south central "Chilean" area. Potato landraces from these two areas can be distinguished, although sometimes with difficulty, by (1) cytoplasmic sterility factors, (2) morphological traits, (3) daylength adaptation, (4) microsatellite markers, and (5) co-evolved chloroplast (cp) and mitochondria (mt) DNA. The Chilean introduction hypothesis originally was proposed because of similarities among Chilean landraces and modern "European" cultivars with respect to traits 2 and 3. Alternatively, the Andean introduction hypothesis suggests that (1) traits 2 and 3 of European potato evolved rapidly, in parallel, from Andean landraces to a Chilean type through selection following import to Europe, and (2) the worldwide late blight epidemics beginning in 1845 in the United Kingdom displaced most existing European cultivars and the potato was subsequently improved by importations of Chilean landraces. We reassess these two competing hypotheses with nuclear microsatellite and cpDNA analyses of (1) 32 Indian cultivars, some of which are thought to preserve putatively remnant populations of Andean landraces, (2) 12 Andean landraces, and (3) five Chilean landraces. Our microsatellite results cluster all Indian cultivars, including putatively remnant Andean landrace populations, with the Chilean landraces, and none with the "old Andigenum" landraces. Some of these Indian landraces, however, lack the cpDNA typical of Chilean landraces and advanced cultivars, indicating they likely are hybrids of Andean landraces with Chilean clones or more advanced cultivars. These results lead us to reexamine the hypothesis that early introductions of potato to Europe were solely from the Andes.

Cluster Analysis↗

Topographic distribution of efferent fibers originating from homotopic or heterotopic transplants: heterotopically transplanted neurons retain some of the developmental characteristics corresponding to their site of origin.

The present study was undertaken to determine whether the topographical distribution of cortical efferents is exclusively dependent on environmental cues or is also controlled by intrinsic factors. For the purpose, we used a sensitive tract-tracing method (Phaseolus vulgaris leucoagglutinin) to compare the pattern of efferent fibers of homotopic and heterotopic transplants of embryonic (E16) neocortex. Our findings indicate that transplants of embryonic sensorimotor cortex placed homotopically in the sensorimotor cortex of newborn rats distribute a set of efferent projections not fundamentally different from that of normal sensorimotor cortex. The pattern of efferents arising from transplants of embryonic occipital cortex heterotopically placed in the sensorimotor cortex of newborns is strikingly different. Heterotopically transplanted neurons: (i) only rarely contact normal targets of the motor cortex; (ii) systematically project towards normal targets of the visual cortex (primary and secondary visual cortical areas, dorsal and ventral lateral geniculate nuclei, lateral dorsal and lateral posterior thalamic nuclei, anterior pretectal nucleus and superficial and intermediate layers of the superior colliculus); (iii) distribute fibers to structures normally receiving fibers from both motor and visual cortices (caudate-putamen, pontine nuclei), either exclusively into the visual cortico-recipient zone of the structure or into both visual and motor cortico-recipient zones. Taken together, these results seem to indicate that the heterotopically transplanted cells have retained certain anatomical characteristics of their locus of origin.

Animals↗

On the origin of vertebrate-type steroids present in Locusta migratoria: do they originate from the food?

1. This study investigates the origin of vertebrate-type steroids which were reported to be present in Locusta migratoria: are the steroids synthesized by the locust or are they derived from the diet, i.e. grass and rolled oats? 2. It is unlikely that the steroids are synthesized by locust tissues. In vitro incubations of eleven different tissues with labeled pregnenolone or androstenedione did not result in androgen or estrogen synthesis respectively. 3. Steroid synthesis was also not detected when tissues were incubated in the presence of the early precursors cholesterol and isopentenyl pyrophosphate. 4. It is unlikely that the steroids are derived from the diet. Feeding experiments indicate that only low amounts of steroids are capable of crossing the gut-body barrier. 5. Injection of testosterone in the hemolymph also resulted in rapid excretion, instead of storage in tissues. 6. Moreover, radioimmunological measurements indicate that vertebrate-type steroids are absent in the food of locusts. 7. Specificity studies indicate that substances other than vertebrate-type steroids are detected by radioimmunoassay in locust tissue extracts. 8. Because vertebrate-type steroids are absent in locust tissues, it can be concluded that vertebrate-type steroids do not have a physiological function in Locusta.

Androstenedione↗

Replication origin of the Bacillus subtilis chromosome determined by hybridization of the first-replicating DNA with cloned fragments from the replication origin region of the chromosome.

The replication origin (ori) on the Bacillus subtilis genome was determined by the hybridization between the first-replicating DNA region and the cloned fragments from the ori region. The first-replicating DNA region was labeled specifically by [3H]thymidine in the presence of an inhibitor for DNA polymerase during a synchronous initiation of the chromosomal replication by germinating spores starved for thymine, and isolated by a sucrose density gradient centrifugation. Most of the labeled DNA molecules are small in size (up to 1000 bases long). The 45-kb ori region was cloned first in a lambda Charon vector and then subcloned in pBR vectors. Restriction fragments from these cloned DNAs were purified by electrophoresis in agarose gels. Only one region within the 45-kb ori region shows strong hybridization with the first-replicating DNA. Restriction fragments from this region were cloned in a phage M13 vector and separated into complementary strands. Hybridization of the labeled DNA with these cloned single-stranded fragments revealed that one site of the ori is located in each strand and they are some 2-kb apart from each other. Replication starts from these sites and proceeds inwards to pass each other.

Bacillus subtilis↗