Assessment of biology investigations

The restricted range of biology investigations submitted for assessment in England and Wales, almost exclusively laboratory-based and with very little fieldwork, can be seen as a consequence of Sc1 being perceived as a skills-based performance model. An alternative approach to procedural understanding conceptualises investigations as the process of utilising a knowledge base, the Concepts of Evidence. Four biology investigations set in different contexts are analysed in this paper and the Concepts of Evidence used are shown to be very similar for each. However, the sequence in which ideas are used and actions occur differs between lab-based investigations and fieldwork. A case is made for the assessment of investigations against the Concepts of Evidence in written tests as being potentially a more reliable and valid way of assessing the ideas used in all types of biology investigations, thus reducing the distorting effect of assessment on the curriculum.     

Laboratory and radiological investigations in general practice. I-Type requested and rate of use.

The use that 30 general practitioners in four group practices made of open access laboratory and radiological facilities was studied for one year. We were particularly interested in whether general practitioners hoped to exclude rather than confirm abnormality when requesting investigations. All but two of the general practitioners studied used investigations to exclude abnormality to a greater extent than to confirm it. The rate at which the practices investigated patients and the number of investigations requested were appreciably different and were different for individual general practitioners, part time general practitioners requesting more investigations than trainees and full time general practitioners. Haematological investigations accounted for over 30% of requests for investigations in all but one practice, biochemical investigations being requested as often as bacteriological investigations in two of the four practices. The ratio of expected to unexpected results varied among general practitioners; no general practitioner had more unexpected results and the range of ratios was similar for full time and part time general practitioners and for trainees. The proportion of patients with abnormalities uncovered by each practice increased disproportionately as the use of investigations increased, supporting a higher rather than lower rate of investigation among general practitioners. Compared with the results of other studies the use of the radiological facilities available was low. X ray examinations of the skeleton were requested more than chest and contrast media examinations by three of the four practices. Most x ray examinations were used to exclude rather than confirm abnormality by all the practices, with over 85% of results confirming the general practitioner''s initial diagnosis.     

Predictive value of staging investigations in patients with clinical stage I malignant melanoma

We reviewed the charts of 393 consecutive patients referred to the Toronto-Bayview Regional Cancer Centre and the Ontario Cancer Institute between January 1, 1978, and December 31, 1982, with clinical stage I malignant melanoma to determine the predictive value of routine staging investigations. The investigations reviewed included physical examination, liver function tests, radionuclide liver-spleen and bone scans, chest x-ray, whole-lung tomograms, CT chest scans, CT brain scans, and bipedal lymphangiograms. The clinical stage of nine patients was changed, eight as a result of physical examination and one as a result of lymphangiogram. No other investigations detected metastatic melanoma at referral. We recommend that staging investigations for patients referred with clinical stage I malignant melanoma be restricted to a complete physical examination and a baseline chest x-ray for all patients.     

Exclusions and attributions of paternity: practical experiences of forensic genetics and statistics.

The Swedish State Institute for Blood Group Serology is a central government laboratory handling all blood typing in paternity cases in Sweden, each year testing 1,500-2,000 cases using about 13 polymorphisms. Of the accused men, 35%-40% are nonfathers, but in one-man cases (about 78% of all cases), approximately 75% are the true fathers. Exclusions appear to be distributed as expected from allele frequencies, and the paternity probability of nonexcluded men is assessed with a Bayesian approach. Some cases are retested in extended investigations which raise theoretical exclusion capability from about 87% to about 99%. Both the results of extended investigations and the theoretical consideration of the distribution of paternity probabilities support the use of such positive statistical evidence for the attribution of paternity.     

Prostatism: how useful is routine imaging of the urinary tract?

The clinical effects of routinely imaging the renal tract (by intravenous urography and ultrasonography) were evaluated prospectively in 128 consecutive patients with prostatism. Patients with haematuria, previous renal disease, or infection were excluded. Urologists completed a standard questionnaire in the patient''s notes stating the diagnosis and the intended management. The patient then had intravenous urography and abdominal ultrasonography, urine was analysed, and plasma urea and serum creatinine concentrations and acid phosphatase activity were determined. From six months to a year later the eventual management was compared with the intended management to see the effect of these routine investigations on the outcome. For four out of 28 patients whose management was intended to be conservative the decision was changed; for only three of them was this because of the results of urography, ultrasonography, and biochemical determinations. For 31 patients the management was to be decided by cystoscopic findings, and for none of these was the final decision altered by the results from the investigations after the initial consultation. Similarly for five patients who were assessed urodynamically the final management was not changed by the results of these investigations. The planned management was changed in three of the remaining 64 patients but not because of the results of the initial investigations.Thus no indication was found for either routine urography or ultrasonography, but the total abandonment of imaging of the renal tract would be unwise. Patients scheduled for conservative management (about a quarter of the patients in this study) should have ultrasonography to detect unsuspected hydronephrosis, but in all other patients urography or ultrasonography, or both, is an unhelpful ritual. Moreover, urography is becoming more expensive, and has a recognised (albeit small) mortality.     

Morphological and physiological characterization of fiber types in the iliofibular muscle of Rana esculenta]

In both longitudinal and cross sections of the M. iliofibularis of Rana esculenta three types of muscle fibres are identified by means of light and electron microscopy. These fibretypes called A-, B- and C-fibres are according to the fibres of m. rectus abdominis of the frog. They can be compared with the fibres of the m. rectus abdominis of rat and mouse. But there is another distribution of the fibretypes A, B and C in the m. iliofibularis and in the m. rectus abdominis. The m. iliofibularis is divided into two parts called "Tonusbündel" and "nichttonischer Teil" by means of their reaction to acetylcholine. The surface of the "Tonusbündel" consists of A-, B- and C-fibres while its inside is onlyformed by A- and B-fibres. They continue the "Tonusbündel" in the "nichttonischer Teil". This part chiefly consists of A-fibres. In cross sections their myofibrils are larger in their extent than the A-fibres known before. Therefore the A-fibretype has to be distinguished into two A-fibres: A1 and A2. The new one is called A2-fibre. A1-fibre is described in the "Tonusbündel" and in further investigations. The difference between the two fibres can be understood as a greater manifestation of power of the A1-fibre. The surface of the "nichttonischer Teil" of the m. iliofibularis consists of A2-fibres which easily could be found opposite the "Tonusbündel". At this point in contrary to the "Tonusbündel" could be found a defined morphological substrate for physiological investigations. The different reactions of "Tonusbündel" and "nichttonischer Teil" to acetylcholine could only be explained by the sum of reactions of all fibretypes in each bundle in correspondence with the reaction of the fibres in the neighbour bundle. But their different behaviour by summer- and winterfrogs is unknown. Therefore it is to discuss whether it is allowed to refer generally the results to "muscle" or "musclefibre" got from frogs living in cooled rooms. It is known in literature that not all results of physiological investigations can be interpreted with the two fibre- theorie ("twitch" and "slow") of muscle. Those not interpretable physiological results could be associated to the B-fibre can not be explained by morphological methods but must be proofed by physiological investigations. In tables are summerised morphological criteria of the three types and it is tried to associate the physiological qualities known from literature. Besides there is summerised the usual nomenclature with the first citations.     

Cryptosporidiosis: biology,pathogenesis and disease

Ninety-five years after discovery and after more than two decades of intense investigations, cryptosporidiosis, in many ways, remains enigmatic. Cryptosporidium infects all four classes of vertebrates and most likely all mammalian species. The speciation of the genus continues to be a challenge to taxonomists, compounded by many factors, including current technical difficulties and the apparent lack of host specificity by most, but not all, isolates and species.     

Skeletal studies of the people of Sicily: An update on research into human remains from archaeological contexts

Human skeletal remains, commonly at the focus of the archaeological investigations of cemeteries, recently have become of increasing importance in reconstructing the culture history of Sicily. A review of the history of osteological investigations on Sicily, including note of recent studies, demonstrates the considerable progress made in recent years and provides future researchers with indications of directions that are available to be taken. This list provides an update to an earlier study (Becker 1995–96). We now have a more useful indication of the extent of human skeletal material now available from Sicilian archaeological sites, from all periods, that may be used in comparative studies.     

Novel perspectives in wood certification and forensics: dry wood as a source of DNA

The importance of wood for human societies can hardly be understated. If dry wood were amenable to molecular genetic investigations, this could lead to major applications in wood forensics, certification, archaeology and palaeobotany. To evaluate the potential of wood for molecular genetic investigations, we have attempted to isolate and amplify, by PCR, DNA fragments of increasing size corresponding to all three plant genomes from different regions of 10 oak logs. Stringent procedures to avoid contamination with external DNA were used in order to demonstrate the authenticity of the fragments amplified. This authenticity was further confirmed by demonstrating genetic uniformity within each log using both nuclear and chloroplast microsatellites. For most wood samples DNA was degraded, and the sequences that gave the best results were those of small size and present in high copy number (chloroplast, mitochondrial, or repeated nuclear sequences). Both storage conditions and storage duration play a role in DNA conservation. Overall, this work demonstrates that molecular markers from all three plant genomes can be used for genetic analysis on dry oak wood, but outlines some limitations and the need for further evaluation of the potential of wood for DNA analysis.     

Pitfall trapping within enclosures: a method for estimating the relationship between the abundances of coexisting carabid species (Coleoptera: Carabidae)

Pitfall trapping within enclosures is proposed as a method to get a reliable impression of the relationship between the abundances of a number of coexisting carabid species. The investigations were performed during two years in a heavily grazed pasture at Melle (Belgium). On a rather large scale soil samples could be compared with both enclosed and open pitfall catches.
In all cases fenced pitfalls gave ratios between the catches of the different species showing a much better correlation with those from soil samples than the catch ratios from open pitfalls. This method seems especially suitable to compare the relative abundances of a number of carabid species in short term investigations during periods of peak activities.     

The etiological structure of acute bacterial meningitis in different regions]

In 1985-1989 the etiological structure of acute bacterial meningitides (ABM) in children was studied in 4 largest industrial cities in different regions of the European part of the former USSR, as well as in 2 industrial cities of western Siberia. Due to the common methodological approach used in all investigations, comparable data were obtained in all cities. These investigations revealed that meningococci caused 53.0-86.7% of all cases of ABM in children, which corresponded to moderately increased morbidity rate in meningococcal infection (3.9-11.0 cases per 100,000 of the population, mostly 5.0-7.0 cases) in these cities with its progressive decrease during 3-4 years of observation. The gradual change of meningococci from group A, prevailing in the '70s and early '80s, to group B and in some cases the appearance of group C meningococci, accompanied by a decrease in morbidity rate, were noted. In St. Petersburg the indices of ABM morbidity in children aged up to 5 years for 1987 and 1988, caused by Haemophilus influenzae (0.74 and 4.13) and pneumococci (3.23 and 4.86), could be calculated. A great number of ABM cases of unclear etiology (15.9-33.3%) suggests that the number of ABM cases caused by these two infective agents was underestimated.     

Ultrasonography compared with intravenous urography in the investigation of adults with haematuria.

OBJECTIVE--To compare ultrasonography with intravenous urography in the investigation of adults with haematuria. DESIGN--Prospective study entailing the examination of all patients with both investigations concurrently. The investigations were performed independently on routine lists by different duty radiologists. Each was aware of the details of the request form but not of the findings of the other investigation. SETTING--Radiology department of a teaching hospital. PATIENTS--155 Consecutive adult patients (aged 18-93) referred from general practitioners and hospital outpatient clinics with a history of haematuria. FOLLOW UP--When results of both examinations proved normal no clinical or radiological follow up was sought. All abnormal findings of either investigation were correlated with results of subsequent imaging studies or operative findings. RESULTS--81 Patients (52%) had normal findings on urography and ultrasonography. Overall, the findings of ultrasonography concurred with those of urography in 144 cases (93%). Among the discrepant findings of the two investigations ultrasonography missed two ureteric calculi; one was in a non-dilated ureter, and in the other case ultrasonography detected the secondary ureteric dilatation. Ultrasound examination alone detected four bladder tumours not visible on urography with sizes ranging from 5 to 21 mm, representing one fifth of the 20 cystoscopically proved bladder tumours detected in the series. Ultrasonography detected all the 22 neoplastic lesions discovered in the study (20 bladder, two renal). Ultrasonography clarified the nature of renal masses evident in three urograms (simple cysts). CONCLUSIONS--Ultrasonography is a safe and accurate method of investigating the urinary tract in adults with haematuria. When combined with a single plain abdominal radiograph it proved to be superior to urography as the primary imaging study in this series. Ultrasonography should certainly be preferred to urography if cystoscopy is not planned. No urothelial tumours of the upper urinary tract were found in the series, reflecting their rarity. For those patients in whom ultrasonography and plain radiography have shown no abnormality and in whom cystoscopic appearances are normal urography would be advisable to exclude urothelial tumours of the upper urinary tract.     

Histochemical determination of peroxidases in isolated leukocytes and lymphocytes in human blood

These investigations show that beside granulocytes human lymphocytes, too contain peroxidase, which is visible after reaction with benzidine. It can be established that all of the phenoloxidase positive cells contain also peroxidase.     

Annual variations of biotic integrity in the upper Yangtze River using an adapted index of biotic integrity (IBI)

Adaptive modification and use of Karr's index of biotic integrity (IBI) for the upper Yangtze River, including 12 metrics in five categories, have typically occurred in line with the data collected by 6-year commercial fisheries investigation. These investigations were undertaken annually in four sections of the Upper Yangtze main channel between 1997 and 2002. These four monitoring sections (Yibin – YB, Hejiang – HJ, Mudong – MD, and Yichang – YC) were selected because they represent the part of the river that will be covering a 1000 km stretch that includes the future Three Gorges Reservoir (TGR), upstream of the Three Gorges Dam (TGD), an area influenced by the construction of TGD. In addition, historical data were used to show changes in the watershed by comparison with field investigations recently. The biotic integrity of the four sections were calculated and classified into different levels annually for recognizing its spatial and temporal variations. It was observed that IBI scores were becoming lower diminishingly since 1997 in all the four sections. Because all the data were collected before the impoundment of the Three Gorges Reservoir, it is obvious that human activities, especially over-fishing, must be crucial factor instead of damming in the upper Yangtze River in that period.     

A general modeling and visualization tool for comparing different members of a group: application to studying tau-mediated regulation of microtubule dynamics

Background  

Innumerable biological investigations require comparing collections of molecules, cells or organisms to one another with respect to one or more of their properties. Almost all of these comparisons are performed manually, which can be susceptible to inadvertent bias as well as miss subtle effects. The development and application of computer-assisted analytical and interpretive tools could help address these issues and thereby dramatically improve these investigations.     

Costs of unnecessary tests.

The relative importance of the history, examination, and routine and special investigations has been assessed in the diagnosis and management of 630 medical outpatients. The history was the most important factor in both diagnosis and management in cardiovascular, neurological, respiratory, urinary, and other miscellaneous problems, and decided 56% of all diagnoses and 46% of all management. Examination findings were of more limited value, accounting for only 17% of diagnostic and 17% of management decisions overall. Routine haematology and urine examinations were of minimal value, contributing to less than 1% of all diagnoses. Special investigations decided most of the diagnoses and management in alimentary and endocrine problems, but were less helpful in problems affecting all other systems. If a local survey in the Trent Region reflected the pattern of medical outpatient practice nationally, then pounds 1.25 million could be saved annually if routine investigation was discontinued on all patients whose problem had already been diagnosed on the basis of the history and the clinical examination.     

Myosin subfragment-1: structure and function of a molecular motor: Current opinion in structural biology 1993, 3:944–952

The ability for directed movement is a fundamental process of all living systems. Molecules designed for such purposes are ubiquitous in eukaryotic cells and have been the focus of intense investigations for many years. Highlighted in this report is the three-dimensional structure of the myosin motor domain—the first such motor protein to be examined by single-crystal X-ray diffraction analysis.     

Applications of fluorescence spectroscopy to molecular cytogenetics

Phenomena studied by fluorescence spectroscopy, including differential perturbations of dye fluorescence by variations in DNA composition and interdye energy transfer, can be applied to cytological studies of chromosome structure, replication, and repair. When combined with fluorescence-activated flow sorting, fluorescent differentiation between metaphase chromosomes can be exploited to obtain recombinant DNA libraries enriched for all or parts of individual chromosomes. Cloned DNA segments from such libraries continue to find application in studies of human chromosome structure and function and in molecular linkage analyses, thus leading to molecular genetic investigations of human disease states.     

Comparison of microarray and sage techniques in gene expression analysis of human glioblastoma

To enhance glioblastoma (GB) marker discovery we compared gene expression in GB with human normal brain (NB) by accessing SAGE Genie web site and compared obtained results with published data. Nine GB and five NB SAGE-libraries were analyzed using the Digital Gene Expression Displayer (DGED), the results of DGED were tested by Northern blot analysis and RT-PCR of arbitrary selected genes. Review of available data from the articles on gene expression profiling by microarray-based hybridization showed as few as 35 overlapped genes with increased expression in GB. Some of them were identified in four articles, but most genes in three or even in two investigations. There was found also some differences between SAGE results of GB analysis. Digital Gene Expression Displayer approach revealed 676 genes differentially expressed in GB vs. NB with cut-off ratio: twofold change and P < or = 0.05. Differential expression of selectedgenes obtained by DGED was confirmed by Northern analysis and RT-PCR. Altogether, only 105 of 955 genes presented in published investigations were among the genes obtained by DGED. Comparison of the results obtained by microarrays and SAGE is very complicated because authors present only the most prominent differentially expressed genes. However, even available data give quite poor overlapping of genes revealed by microarrays. Some differences between results obtained by SAGE in different investigations can be explained by high dependence on the statistical methods used. As for now, the best solution to search for molecular tumor markers is to compare all available results and to select only those genes, which significant expression in tumor combined with very low expression in normal tissues was reproduced in several articles. 105 differentially expressed genes, common to both methods, can be included in the list of candidates for the molecular typing of GBs. Some genes, encoded cell surface or extra-cellular proteins may be useful for targeting gliomas with antibody-based therapy.