Uniform Nomenclature Research Articles

Reply: RCT of real versus placebo acupuncture in IVF

Sir, We refer to the letter by Renckens addressed at our recent publication (So et al., 2009) on the use of acupuncture in IVF treatment, stating that Human Reproduction should not publish papers on absurd forms of treatment such as acupuncture. Although there are no particular comments directed to us, we would like to respond to the opinion stated in the letter and express our views on Traditional Chinese Medicine (TCM) and acupuncture. (i) The WHO booklet on Standard Acupuncture Nomenclature aims to develop a uniform nomenclature in acupuncture so as to achieve global agreement on a standard acupuncture nomenclature. This has greatly facilitated research and exchange of information in this area. However, it should be clarified that the purpose of this booklet is not to correlate the acupoints with the well-known anatomical landmarks in Western Medicine. (ii) Different medical systems may have different developments and philosophies. The theory of Yin-Yang used in TCM is certainly different from that of Western Medicine. Although anatomical correlates of acupoints are still not demonstrated, we should not reject the existence of the acupoints and the effects of TCM in clinical trials. (iii) IVF is not listed as an indication in the WHO report ‘Acupuncture: review and analysis of reports on controlled clinical trials’ because the first randomized study on acupuncture in IVF (Paulus et al., 2002) was published in 2002. Other relevant randomized studies were published in 2006 and several metaanalyses on acupuncture in IVF were published in 2008. There are many meta-analyses on acupuncture in the Cochrane library. (iv) In our paper, we put down the rationale of choosing the acupoints, which is based on the TCM theory. This intends to give the readers more information about Chinese Medicine. In order for the reader to appreciate the effects of acupuncture, we determined outcome measures that are very well defined, scientifically valid and commonly used in studies in Western Medicine. (v) We strongly believe that well-conducted RCT, especially double blind, is still the golden method to examine the effectiveness of a therapy, whether the therapy is believed by some to be absurd or not. We will be delighted to learn any other means which are better to study absurd claims. It is also unfair to say that a therapy is absurd just because it is not consistent with our own beliefs. Science has advanced because scientists have continued to challenge and change some of the established concepts by properly conducted experiments. In the assessment of the efficacy of a therapy, a properly conducted RCT is the best experimental approach to prove or refute the efficacy of a form of therapy. (vi) As the design of studies including those on TCM is evolving and improving, it seems unfair to point out the methodological weakness based on evidence published before 1989. There were also many examples of clinical trials conducted in Western countries with methodological weaknesses. Again, we should always keep the most updated evidence in Science. It is well known that studies with negative results are more difficult to be published than those with positive results. This may be related to the publication policy of journals, rather than where the papers come from. We agree that journals nowadays should not publish papers with serious methodological problems but we strongly disagree that journals do not publish properly conducted RCT on therapies which may appear ‘absurd’ to some readers. Scientific development will be suffocated if journals adopt this approach. We are of the opinion that well-conducted research in TCM should be continued in order to confirm or refute the effectiveness of TCM in clinical practice. The results of these studies, whether positive or not, should be published in peer-reviewed journals. Last but not least, we thank the reader for the comment which is a reminder that we must continue to conduct studies in the highest scientific standard.

Conservation of Neotropical Herpetofauna: Research Trends and Challenges

The Neotropics harbor between 30−50% of the world's herpetofauna. However, little is known about the ecology and natural history of many species, making conservation strategies difficult to plan. After reviewing published papers on world herpetofauna conservation, it was shown that conservation biology has a low impact factor in scientific journals in comparison with other related disciplines such as evolutionary biology and ecology. Moreover, herpetology has one of the lowest impact factors within the biological sciences journals. The number of publications on amphibian and reptile conservation has increased in recent years; however, only 31% of the papers on herpetofaunal conservation have been published in high impact journals. There are many challenges to overcome in the conservation of the Neotropical herpetofauna. Uniform and stable taxonomic nomenclature is critical to avoid overestimation of species richness and diversity for conservation assessments, and in the context of legal proceedings. Herpetofaunal research needs to be conducted within the appropriate socio-political and economic framework, in order to effectively implement conservation area networks. It is important to reevaluate the role of protected area systems in ensuring the persistence of communities and populations, and to identify strategies and future conservation priorities, based on climate-change scenarios. Population and community studies at different spatial and temporal scales are necessary to understand herpetofauna responses to anthropogenic disturbances, habitat loss and fragmentation, edge and matrix effects, and their synergy with micro-climatic gradients, emergent diseases and shifting patterns of genetic diversity. One of the biggest challenges for herpetofaunal conservation science in the neotropics is to control habitat loss and increase landscape connectivity along altitudinal gradients, while at the same time control species invasion that alter native species' interactions and spread emergent diseases (e.g. Chytridiomycosis) facilitated by climate change.

Identification of pseudouridine methyltransferase in Escherichia coli.

In ribosomal RNA, modified nucleosides are found in functionally important regions, but their function is obscure. Stem-loop 69 of Escherichia coli 23S rRNA contains three modified nucleosides: pseudouridines at positions 1911 and 1917, and N3 methyl-pseudouridine (m(3)Psi) at position 1915. The gene for pseudouridine methyltransferase was previously not known. We identified E. coli protein YbeA as the methyltransferase methylating Psi1915 in 23S rRNA. The E. coli ybeA gene deletion strain lacks the N3 methylation at position 1915 of 23S rRNA as revealed by primer extension and nucleoside analysis by HPLC. Methylation at position 1915 is restored in the ybeA deletion strain when recombinant YbeA protein is expressed from a plasmid. In addition, we show that purified YbeA protein is able to methylate pseudouridine in vitro using 70S ribosomes but not 50S subunits from the ybeA deletion strain as substrate. Pseudouridine is the preferred substrate as revealed by the inability of YbeA to methylate uridine at position 1915. This shows that YbeA is acting at the final stage during ribosome assembly, probably during translation initiation. Hereby, we propose to rename the YbeA protein to RlmH according to uniform nomenclature of RNA methyltransferases. RlmH belongs to the SPOUT superfamily of methyltransferases. RlmH was found to be well conserved in bacteria, and the gene is present in plant and in several archaeal genomes. RlmH is the first pseudouridine specific methyltransferase identified so far and is likely to be the only one existing in bacteria, as m(3)Psi1915 is the only methylated pseudouridine in bacteria described to date.

Assessment of 1p/19q deletions by fluorescence in situ hybridization in gliomas

This study assessed the efficacy of FISH for detecting 1p/19q deletion in gliomas on 77 paraffin-embedded tissue samples, of which 42 cases (55%) were positive for 1p/19q codeletion; 7 of the 42 had a previous history of glioma. In one case, analysis failed. The remaining 34 cases were negative; of these, three had a previous history of glioma and one had the reverse 1q/19p deletion. A majority of the 10 recurrent gliomas had progressed, and 70% had a 1p/19q deletion. The signal pattern in a majority of 1p/19q codeletion cases was a single red marker signal and two green reference signals (1R2G) for both probe sets. One case had a different signal pattern for chromosomes 1 and 19 (1R2G and 2R4G), as seen in polysomy cells. Three cases had two target and four control signals (2R4G), as seen in tetraploid cells. Eleven had complex signal patterns seen in diploid and polyploid cells (1R2G/< nR nG). A majority of these complex cases (8 of 11, or 73%) had high-grade oligodendroglioma ( n = 4) or oligoastrocytoma ( n = 4). The frequency of 1p/19q combined deletion in oligodendroglioma ( n = 40), oligoastrocytoma ( n = 21), and astrocytoma ( n = 8) was 65, 60, and 25%, respectively. Elucidated in this paper are the various FISH signal patterns observed in gliomas and a need for a uniform nomenclature for improved diagnosis.

Patellar hypertension syndrome--nomenclature, diagnosis and therapy

Complaints in the area of the patella have been abundantly described in the literature. However, a uniform nomenclature with regard to either diagnosis or therapy does not exist. With the help of a standardized measuring method (intrapatellar pressure measurement and provocation test), it is possible to describe and classify patellar pain. An intrapatellar pressure increase over 25 mmHg and/or a positive provocation test defines the term of Patella Hypertension Syndrome. Within a prospective study we carried out a special intraosseous drilling in 20 cases with the typical symptoms of the Patella Hypertension Syndrome. The drilling, which was carried out via the Hoffa fat body from distal, resulted in a distinct alleviation of symptoms in all cases and even in a complete absence of pain in most cases. This phenomenon was objectified by a pressure-check-up after 6 weeks, 6 months and 1 year following the drilling. In all 20 cases so far examined a decrease of between 40-70% of the original pressure level was achieved. In all cases the postoperative artificial pressure increase (provocation test) of the intraosseous pressure did not lead to the typical pain symptoms. We therefore have a relatively minor operation at our disposal enabling us to achieve an impressive therapeutic success, in cases where conventional treatment was neither causal nor successful.

The Geriatric Minimum Data Set for clinical trials (GMDS).

To overcome the weak evidence base coming from often poor and insufficient clinical research in older people, a minimum data set to achieve harmonisation is highly advisable. This will lead to uniform nomenclature and to the standardisation of the assessment tools. Our primary objective was to develop a Geriatric Minimum Data Set (GMDS) for clinical research. Investigators from 33 leading Research Centres in Europe (selected based on pre-defined criteria), agreed to establish GerontoNet, a network for research collaboration. Following a systematic review of literature performed before the meeting, the expert panel identified 79 functional, cognitive, nutritional and social statements. Of the initial 79 statements, 49 were found appropriate for a GMDS. After an additional stage of evaluation, a 25-item data set was proposed as the minimum set of information to be included in any future clinical trial involving older people. The GMDS covers 7 domains: general information including data on clinical diagnosis and medication use (5 items), functional performance (5 items), cognitive and emotional status (4 items), cardiovascular risk profile (3 items), nutritional status (3 items), biochemical parameters (1 set and 1 item), and social status (3 items). The proposed GMDS provides an enhanced opportunity for research in elderly populations with appropriate outcome measures, and would greatly facilitate meta-analysis of relevant clinical trials.

Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008)

AbstractExpanded definitions of rotaxanes and pseudorotaxanes, their components, and other terms concerning rotaxanes are given. The uniform classification and nomenclature principles for naming different types of rotaxanes and pseudorotaxanes are described and illustrated with examples. Recommendations are provided for unambiguous description of rotaxane isomerism with special descriptors that include information about position of rotaxane components.

Advantages of standardizing vaccine and antibody nomenclature

In the late 1970s, practitioners struggled to legibly write generic names such as diphenylhydantoin and dioctyl sodium sulfosuccinate. They were delighted when authorities switched to the simpler names (phenytoin and docusate sodium, respectively) that we use today.Unfortunately, a similar problem exists today with respect to vaccine names. Some of these have grown to cumbersome length, measured in words, not syllables. Some vaccine names could create misunderstanding and error due to inconsistencies or mistaken emphasis. Superfluous words clutter product labels, especially single-dose vials and prefilled syringes. If shorter names were available, font size could be increased, making visualization easier. Long names also make it more difficult to focus on what is important.This article summarizes my recent commentary in Pharmacopeial Forum that proposed a uniform nomenclature for vaccines and polyclonal antibodies.1 Review of nonproprietary vaccine and antibody names revealed several inadequacies. The names of vaccines licensed by the Food and Drug Administration (FDA) inconsistently use the words “combined,” “inactivated,” “live,” and “virus” and terms designating antigenic valency, microbial strain, production media, and target population. Concepts such as adsorbed, recombinant, and conjugate could be revised to deliver more information in less space. Among polyclonal immune globulin products, however, few inconsistencies in nomenclature were noted.

Evidence for 26 distinct acyl-coenzyme A synthetase genes in the human genome

Acyl-coenzyme A synthetases (ACSs) catalyze the fundamental, initial reaction in fatty acid metabolism. "Activation" of fatty acids by thioesterification to CoA allows their participation in both anabolic and catabolic pathways. The availability of the sequenced human genome has facilitated the investigation of the number of ACS genes present. Using two conserved amino acid sequence motifs to probe human DNA databases, 26 ACS family genes/proteins were identified. ACS activity in either humans or rodents was demonstrated previously for 20 proteins, but 6 remain candidate ACSs. For two candidates, cDNA was cloned, protein was expressed in COS-1 cells, and ACS activity was detected. Amino acid sequence similarities were used to assign enzymes into subfamilies, and subfamily assignments were consistent with acyl chain length preference. Four of the 26 proteins did not fit into a subfamily, and bootstrap analysis of phylograms was consistent with evolutionary divergence. Three additional conserved amino acid sequence motifs were identified that likely have functional or structural roles. The existence of many ACSs suggests that each plays a unique role, directing the acyl-CoA product to a specific metabolic fate. Knowing the full complement of ACS genes in the human genome will facilitate future studies to characterize their specific biological functions.

Proposed Classification for the Transbasal Approach and Its Modifications

The transbasal approach offers extradural exposure of the anterior midline skull base transcranially. It can be used to treat a variety of conditions, including trauma, craniofacial deformity, and tumors. This approach has been modified to enhance basal access. This article reviews the principle differences among modifications to the transbasal approach and introduces a new classification scheme. The rationale is to offer a uniform nomenclature to facilitate discussion of these approaches, their indications, and related issues.

Safety assessment of dairy microorganisms: Bacterial taxonomy

Safety assessment requires uniform and reproducible nomenclature schemes for all the micro-organisms deliberately added in fermented food products. The QPS approach described by EFSA is based on the identity of an isolate at the highest taxonomic unit that is appropriate for the purpose for which the evaluation is intended. This depends upon the body of knowledge available for the micro-organism to be assessed and upon the nature of the micro-organism being assessed. Species identification is the fundamental unit of biological classification and is critical for describing, understanding and comparing biological diversities at different levels among ecological niches. Accurate taxonomic identification of a micro-organism is essential for assessing safety assessment, and this section describes current and advanced knowledge on bacterial taxonomy.

Adolphe Quetelet (1796 1874) the average man and indices of obesity

The quest for a practical index of relative body weight that began shortly after actuaries reported the increased mortality of their overweight policyholders culminated after World War II, when the relationship between weight and cardiovascular disease became the subject of epidemiological studies. It became evident then that the best index was the ratio of the weight in kilograms divided by the square of the height in meters, or the Quetelet Index described in 1832. Adolphe Quetelet (1796-1874) was a Belgian mathematician, astronomer and statistician, who developed a passionate interest in probability calculus that he applied to study human physical characteristics and social aptitudes. His pioneering cross-sectional studies of human growth led him to conclude that other than the spurts of growth after birth and during puberty, 'the weight increases as the square of the height', known as the Quetelet Index until it was termed the Body Mass Index in 1972 by Ancel Keys (1904-2004). For his application of comparative statistics to social conditions and moral issues, Quetelet is considered a founder of the social sciences. His principal work, 'A Treatise of Man and the development of his faculties' published in 1835 is considered 'one of the greatest books of the 19th century'. A tireless promoter of statistical data collection based on standard methods and definitions, Quetelet organized in 1853 the first International Statistical Congress, which launched the development of 'a uniform nomenclature of the causes of death applicable to all countries', progenitor of the current International Classification of Diseases.

Divergences in diagnosing nodular breast lesions of noncarcinomatous nature

Nodular breast lesions of noncarcinomatous origin are often of fibroepithelial origin. They may cause classification problems when they are hypocellular or hypercellular; the latter setting may also raise the differential diagnosis of phyllodes tumors. Thirty equivocal nodular breast lesions were collected and one hematoxylin and eosin slide from each was assessed by six pathologists with special interest in breast pathology. The overall reproducibility of classifying these lesions into categories of fibroadenoma, phyllodes tumor or anything else was moderate (kappa value: 0.48). The lack of a uniform nomenclature was not felt disturbing for hypocellular lesions, but the discordant diagnosis of tumors resembling or representing phyllodes tumors was acknowledged to require intervention, such as more obvious implication of guidelines and quality assurance programs aiming at assessing diagnoses and prognostic parameters.

Multilocus Sequence Typing of Bacteria

Multilocus sequence typing (MLST) was proposed in 1998 as a portable, universal, and definitive method for characterizing bacteria, using the human pathogen Neisseria meningitidis as an example. In addition to providing a standardized approach to data collection, by examining the nucleotide sequences of multiple loci encoding housekeeping genes, or fragments of them, MLST data are made freely available over the Internet to ensure that a uniform nomenclature is readily available to all those interested in categorizing bacteria. At the time of writing, over thirty MLST schemes have been published and made available on the Internet, mostly for pathogenic bacteria, although there are schemes for pathogenic fungi and some nonpathogenic bacteria. MLST data have been employed in epidemiological investigations of various scales and in studies of the population biology, pathogenicity, and evolution of bacteria. The increasing speed and reduced cost of nucleotide sequence determination, together with improved web-based databases and analysis tools, present the prospect of increasingly wide application of MLST.

Kutane Lymphome

Cutaneous lymphomas are a heterogeneous group of clonal proliferations of T and B lymphocytes with various clinical manifestations and prognosis. The new EORTC WHO classification of cutaneous T- and B-cell lymphomas provides a uniform nomenclature based on clinical, histologic, cytologic and molecular biological features. Accurate classification is a prerequisite for uniform therapeutic concepts. For office-based dermatologist, more than 50% of the therapies deal with classic forms of cutaneous T-cell lymphomas, type mycosis fungoides. In recent years the paradigm for the therapy of cutaneous T-cell lymphomas has changed. Since early aggressive treatment with cytostatic agents does not increase the response rate or overall survival, a commonly accepted stage-adapted therapy is recommended. In this review the current status of the therapy of cutaneous lymphoma is described in detail.

Histopathologic Findings of Malformations of Cortical Development in an Epilepsy Surgery Cohort

Malformations of cortical development (MCDs) are an important cause of pharmacoresistent epilepsy and are frequently diagnosed in surgical pathology. The lack of uniform tissue processing and standard histopathologic nomenclature to describe MCDs has resulted in diagnostic ambiguity. To describe the immunohistochemical findings of MCDs from a relatively large surgical epilepsy cohort and incorporate terminology that more adequately reflects the histopathologic findings into a contemporary classification of MCD. Utilizing the Mayo Clinic Rochester Surgical Pathology Database and patient records, 53 patients with previous intractable epilepsy and a known malformation of cortical development were identified. All of the cohort's paraffin embedded surgical specimens were resectioned and stained with hematoxylin-eosin, Luxol fast blue/cresyl violet, neurofilament protein, and glial fibrillary acidic protein. Each specimen was reviewed histologically and categorized according to a proposed focal MCD classification scheme that substitutes cytoarchitectural dysmorphism for cortical dysplasia and architectural disorganization for microdysgenesis. An MCD was recognized in 49 patients and grouped into 1 of the following 4 categories: (1) cytoarchitectural dysmorphism with balloon cells (n = 19), (2) cytoarchitectural dysmorphism without balloon cells (n = 12), (3) architectural disorganization (n = 8), or (4) polymicrogyria (n = 9). The histopathologic features of focal MCD in a large epilepsy surgical cohort by using practical immunohistochemistry and a contemporary MCD classification scheme are described. It is proposed that the term focal cortical dysplasia be renamed as focal malformations of cortical development.

Histopathologic findings of malformations of cortical development in an epilepsy surgery cohort.

Abstract Context.—Malformations of cortical development (MCDs) are an important cause of pharmacoresistent epilepsy and are frequently diagnosed in surgical pathology. The lack of uniform tissue processing and standard histopathologic nomenclature to describe MCDs has resulted in diagnostic ambiguity. Objective.—To describe the immunohistochemical findings of MCDs from a relatively large surgical epilepsy cohort and incorporate terminology that more adequately reflects the histopathologic findings into a contemporary classification of MCD. Design.—Utilizing the Mayo Clinic Rochester Surgical Pathology Database and patient records, 53 patients with previous intractable epilepsy and a known malformation of cortical development were identified. All of the cohort's paraffin embedded surgical specimens were resectioned and stained with hematoxylin-eosin, Luxol fast blue/cresyl violet, neurofilament protein, and glial fibrillary acidic protein. Each specimen was reviewed histologically and categorized according...

The classification, functions and clinical use of different isoforms of HCG

HCG is composed of two subunits, HCGalpha and HCGbeta. During early pregnancy, HCG stimulates progesterone production in the corpus luteum, and injection of HCG is widely used to induce ovulation in assisted reproduction treatment (ART). Under experimental conditions, the free subunits have been shown to exert functions other than those of HCG, but the relevance of these remains to be determined. Intact HCG, free subunits and degraded forms of these occur in biological fluids, and determinations of these are important for diagnosis and monitoring of pregnancy, pregnancy-related disorders and several types of cancer. Development of optimal methods for the various forms has been hampered by lack of appropriate standards and expression of the concentrations of the various forms in units that are not comparable. Furthermore, the nomenclature for HCG assays is confusing and in some cases misleading. These problems can now be solved; a uniform nomenclature has been established, and new standards are available for HCG, its subunits HCGalpha and HCGbeta, the partially degraded or nicked forms of HCG and HCGbeta, and the beta-core fragment. This review describes the biochemical and biological background for the clinical use of determinations of various forms of HCG. The clinical use of HCG and studies on HCG vaccines are briefly reviewed.

The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase

BackgroundNaturally occurring tRNAs contain numerous modified nucleosides. They are formed by enzymatic modification of the primary transcripts during the complex RNA maturation process. In model organisms Escherichia coli and Saccharomyces cerevisiae most enzymes involved in this process have been identified. Interestingly, it was found that tRNA methylation, one of the most common modifications, can be introduced by S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases (MTases) that belong to two structurally and phylogenetically unrelated protein superfamilies: RFM and SPOUT.ResultsAs a part of a large-scale project aiming at characterization of a complete set of RNA modification enzymes of model organisms, we have studied the Escherichia coli proteins YibK, LasT, YfhQ, and YbeA for their ability to introduce the last unassigned methylations of ribose at positions 32 and 34 of the tRNA anticodon loop. We found that YfhQ catalyzes the AdoMet-dependent formation of Cm32 or Um32 in tRNASer1 and tRNAGln2 and that an E. coli strain with a disrupted yfhQ gene lacks the tRNA:Cm32/Um32 methyltransferase activity. Thus, we propose to rename YfhQ as TrMet(Xm32) according to the recently proposed, uniform nomenclature for all RNA modification enzymes, or TrmJ, according to the traditional nomenclature for bacterial tRNA MTases.ConclusionOur results reveal that methylation at position 32 is carried out by completely unrelated TrMet(Xm32) enzymes in eukaryota and prokaryota (RFM superfamily member Trm7 and SPOUT superfamily member TrmJ, respectively), mirroring the scenario observed in the case of the m1G37 modification (introduced by the RFM member Trm5 in eukaryota and archaea, and by the SPOUT member TrmD in bacteria).

Problems of development of a uniform nomenclature for medical goods

Problems of development of a uniform nomenclature of medical goods are considered. The importance of compliance of the developed uniform nomenclature with numerous existing standards is emphasized. The uniform nomenclature should also be approved by administrative institutions in the field of medicine.