Refining the systematic literature review process—two participant-observer case studies

Systematic literature reviews (SLRs) are a major tool for supporting evidence-based software engineering. Adapting the procedures involved in such a review to meet the needs of software engineering and its literature remains an ongoing process. As part of this process of refinement, we undertook two case studies which aimed 1) to compare the use of targeted manual searches with broad automated searches and 2) to compare different methods of reaching a consensus on quality. For Case 1, we compared a tertiary study of systematic literature reviews published between January 1, 2004 and June 30, 2007 which used a manual search of selected journals and conferences and a replication of that study based on a broad automated search. We found that broad automated searches find more studies than manual restricted searches, but they may be of poor quality. Researchers undertaking SLRs may be justified in using targeted manual searches if they intend to omit low quality papers, or they are assessing research trends in research methodologies. For Case 2, we analyzed the process used to evaluate the quality of SLRs. We conclude that if quality evaluation of primary studies is a critical component of a specific SLR, assessments should be based on three independent evaluators incorporating at least two rounds of discussion.     

Evaluation of two commercial kits for serum gastrin assay, and comparison with a conventional radioimmunoassay procedure

We compared two gastrin radioimmunoassay kits ("Immutope" kit, Squibb & Co.; "Gastrin R.I.A." kit, Schwarz/Mann) to the conventional gastrin radioimmunoassay of Yalow and Berson [Gastroenterology 58, 1 (1970)] as run by us and by a second reference laboratory. Although both kits were found to effectively discriminate above-normal and normal values for serum gastrin, they significantly underestimated very high values (greater than 1500 ng/liter). The Schwarz/Mann kit clearly had a superior quality label (lower nonspecific binding and higher specific activity) and a shorter incubation time. However, the 90-min incubation period cited for their kit caused overestimation of gastrin values in the lower range (5-300 ng/liter), which could be corrected by prolonging the incubation to 24 h. The Squibb antibody had fairly good cross reactivity to all gastrin species tested; the Schwarz/Mann antibody had poor affinity for natural human gastrin G34-II. Good correspondence was found for sera run by both reference laboratories (y = 0.96x + 10, r = 0.997), and values obtained with the Schwarz/Mann kit correlated best (+ 0.815) with those from the conventional radioimmunoassay procedure.     

Inhibition of feline collateral vessel development following experimental thrombolic occlusion

We compared development of feline hindlimb collateral circulation after acute occlusion of the terminal aorta by ligation, thrombus formation, and formation of a "closed" aortic loop containing thromboplastin. Collateral circulation development was assessed by aortograms, scintillation scans, neurological signs following occlusion, measurement of hindlimb muscle blood flow, and forelimb and hindlimb temperature. In cats in which aortic occlusion was the result of ligation or thromboplastin in the aortic loop, paralysis was not evident. Aortograms and scintillation scans indicated hindlimb blood flow. Both muscle temperature and blood flow data indicated that the return of blood flow was rapid. The 5th lumbar artery appears to be the origin of the collateral vessels. The mid-zone component is a dorsal and ventral vertebral route and an epaxial muscle route. The reentry components are the 6th or 7th lumbar arteries. The collateral vessels arise from preexisting collateral vessels. Of those cats in which aortic occlusion was the result of a thrombus, all exhibited paralysis. Aortograms, scintillation scans, muscle temperature, and hindlimb blood flow data indicated reduced hindlimb blood flow. The results suggest that the thrombus has an inhibitory effect on the development of collateral circulation.     

Bypass surgery for vascular disease of the carotid system

A series of 58 operations on 56 patients, in whom a branch of the superficial temporal artery was anastomosed to a branch of the middle cerebral artery (STA-MCA bypass or Yasargil procedure), is reviewed. These operations were performed chiefly for occlussions or for inaccessible stenotic lesions of the internal carotid or middle cerebral arteries. Patency in eight patients operated on from April 1971 through November 1973 was low (25%). Patency in patients operated on since July 1974 has been high (95%). There have been no deaths and no major ischemic strokes attributable to the surgery. The rationale for this procedure is considered in relationship to the anatomy and physiology of the cerebral circulation and the pathogenesis of syndromes of cerebral ischemia. The operation appears to have a low morbidity in good-risk patients. The role of this operation in managing common manifestations of cerebral vascular disease such as focal transient cerebral ischemic attacks (TIAs) and amaurosis fugax, although not fully established, appears encouraging. The procedure seems useful for orthostatic cerebral ischemia caused by multiple occlusions of major extracranial (and intracranial) vessels and, occasionally, for progressing strokes related to internal carotid artery occlusion, both of which are relatively uncommon manifestations of cerebral vascular occlusive disease. It may have application in the rare "slow stroke." The procedure is probably of limited value, if any, in the management of large completed infarcts but may be indicated in selected patients with small infarctions who have preserved most of their cerebral function and who have had evidence of subsequent focal ischemic events. The procedure is useful for bypassing giant aneurysms or basofrontal tumors invading major vessels. It may have a role in the management of fibromuscular disease of the internal carotid artery.     

Hypertext: the next maintenance mountain

Hypertext documents are quickly becoming large, complex, and unwieldy. The paper considers whether lessons learned from software maintenance can be applied to the problem. Since software maintenance is a major problem and since hypertext documents share many of the characteristics of software: structure, development process, and economic value, maintaining hypertext documents is also likely to become a major problem requiring immediate action     

Percutaneous radiologic drainage of pancreatic abscesses

OBJECTIVE: The purpose of our study was to review and report the patient selection, techniques, and results of percutaneous drainage of pancreatic abscesses by retrospective review. MATERIALS AND METHODS: Fifty-nine patients (46 men and 13 women) with a mean age of 44 years old had 80 pancreatic abscesses that were drained percutaneously under radiologic guidance (CT, n = 77; sonography, n = 2; and fluoroscopy, n = 1). Abscesses had a wide spectrum of causes, with alcoholic pancreatitis being most common, trauma second most common, and gallstones third. Ten patients had undergone surgery for pancreatic necrosis or abscess. Patients with pancreatic pseudocysts, necrosis, or acute fluid collections were excluded from this study. RESULTS: Of the 59 patients, 51 (86%) were cured with percutaneous drainage and antibiotic therapy. Of the patients who were not cured with percutaneous drainage, seven required surgery and one underwent repeat percutaneous drainage. In the 59 patients, complications included non-life-threatening bleeding in three patients. Ten of 59 patients (17%) had fistulas that spontaneously formed into the gastrointestinal tract. The duration of catheterization ranged from 4 to 119 days, with a mean duration of 33 days. The rate of mortality at 30 days after completion of percutaneous drainage was 8% (5 of 59). CONCLUSION: Percutaneous drainage was an effective therapy for this defined group of patients with pancreatic abscesses. Factors leading to the relatively high success rate described in this study likely included selection of patients; catheters of adequate size, number, and location; careful follow-up with appropriate catheter manipulations; and an integrated, cooperative approach whereby surgeons were willing to permit drainage to effect its benefits, rather than operating prematurely.     

Determination of 1,3-dichloropropanol in soy sauces by automated headspace gas chromatography-mass spectrometry.

There has been recent concern about the levels of carcinogenic chloropropanols in some soy sauces. We have devised and tested a new automated headspace GC-MS technique for the analysis of 1,3-dichloropropan-2-ol (1,3-DCP) in soy sauce and similar products. The method incorporates the use of cryogenic trapping and a deuterium-labelled internal standard. The limit of detection was 0.003 mg kg(-1). After in-house validation testing, the method was applied to soy sauce samples that had previously been analysed for the related contaminant 3-monochloropropanediol (3-MCPD). 1,3-DCP was detected in 10 of 40 sauces, all of which also contained 3-MCPD. The highest level was just >1 mg kg(-1). There was no correlation between the levels of 1,3-DCP and 3-MCPD.     

Self Organising Maps for variable selection: Application to human saliva analysed by nuclear magnetic resonance spectroscopy to investigate the effect of an oral healthcare product

SOMs (Self Organising Maps) are derived from the machine learning literature and serve as a valuable method for representing data. In this paper, the use of SOMs as a technique for determining the most significant variables (or markers) in a dataset is described. The method is applied to the NMR spectra of 96 human saliva samples, half of which have been treated with an oral rinse formulation and half of which are controls, and 49 variables consisting of bucketed intensities. In addition, three simulations, two of which consist of the same number of samples and variables as the experimental dataset and a third that contains a much larger number of variables, are described. Two of the simulations contain known discriminatory variables, and the remaining is treated as a null dataset without any specific discriminatory variables added. The described SOM method is contrasted to Partial Least Squares Discriminant Analysis, and a list of the markers determined to be most significant using both approaches was obtained and the differences arising are discussed. A SOM Discrimination Index (SOMDI) is defined, whose magnitude relates to how strongly a variable is considered to be a discriminator. In order to ensure that the model is stable and not dependent on the random starting point of the SOM, one hundred iterations were performed and variables that were consistently of high rank were selected. A variety of approaches for data representation are illustrated, and the main theoretical principles of employing SOMs for determining which variables are most significant are outlined. Software used in this paper was written in-house, allowing greater flexibility over existing packages, and tailored for the specific application in hand.     

Probing the stoichiometry and oxidation states of metal centers in iron-sulfur proteins using electrospray FTICR mass spectrometry

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry is used to determine the stoichiometry and oxidation states of the metal centers in several iron-sulfur proteins. Samples are introduced into the ESI source under nondenaturing conditions in order to observe intact metal-containing protein ions. The stoichiometry and oxidation state of the metal or metal-sulfur cluster in the protein ion can be derived from the mass spectrum. Mononuclear metal-containing proteins and [4Fe-4S] centers are very stable and yield the molecular ion with little or no fragmentation. Proteins that contain [2Fe-2S] clusters are less stable and yield loss of one or two sulfur atoms from the molecular species, although the molecular ion is more abundant than the fragment peaks. [3Fe-4S]-containing proteins are the least stable of the species investigated, yielding abundant peaks corresponding to the loss of one to four sulfur atoms in addition to a peak representing the molecular ion. Isotope labeling experiments show that the sulfur loss originates from the [3Fe-4S] center. Negative ion mode mass spectra were obtained and found to produce much more stable [3Fe-4S]-containing ions than obtained in positive ion mode. ESI analysis of the same proteins under denaturing conditions yields mass spectra of the apo form of the proteins. Disulfide bonds are observed in the apoprotein mass spectra that are not present in the holoprotein. These result from oxidative coupling of the cysteinyl sulfur atoms that are responsible for binding the metal center. In addition, inorganic sulfide is found to incorporate itself into the apoprotein by forming sulfur bridges between cysteine residues.     

Double-helix coil for occlusion of large patent ductus arteriosus: evaluation in a chronic lamb model

Glyceraldehyde-3-phosphate dehydrogenase (G3PDH) is often used as a control gene for mRNA expression, however it has been proposed to be overexpressed in all hepatocellular carcinomas (HCC). Equal amounts of tumor and paired normal (T/N) RNA, based on OD260/280 nm, were compared using ethidium bromide staining, poly-T probing, gene-specific dot blot and Northern blots using control probes G3PDH, actin and histone H4. Using mRNA blots 13/20 surgical HCC pairs did not overexpress G3PDH. Those 7/20 intact samples which did appear to overexpress G3PDH on Northern blot could not be detected by poly-T probing of dot blots. The apparent overexpression was not specific for the control gene G3PDH nor for the malignancy HCC. It may represent partial mRNA degradation, or the presence of as yet unknown substances which interfere with absorption at 260/280 nm. We advise caution in selecting human T/N pairs for differential gene expression studies. For HCC, no clinicopathological variables, including cirrhosis, predicted whether a T/N sample pair was likely to be balanced or not.