Smaller sample sizes for phase II trials based on exact tests with actual error rates by trading-off their nominal levels of significance and power

Background: Sample sizes for single-stage phase II clinical trials in the literature are often based on exact (binomial) tests with levels of significance (alpha (α) 80%). This is because there is not always a sample size where α and power are exactly equal to 5% and 80%, respectively. Consequently, the opportunity to trade-off small amounts of α and power for savings in sample sizes may be lost. Methods: Sample-size tables are presented for single-stage phase II trials based on exact tests with actual levels of significance and power. Trade-off in small amounts of α and power allows the researcher to select from several possible designs with potentially smaller sample sizes compared with existing approaches. We provide SAS macro coding and an R function, which for a given treatment difference, allow researchers to examine all possible sample sizes for specified differences are provided. Results: In a single-arm study with P0 (standard treatment)=10% and P1 (new treatment)=20%, and specified α=5% and power=80%, the A’Hern approach yields n=78 (exact α=4.53%, power=80.81%). However, by relaxing α to 5.67% and power to 77.7%, a sample size of 65 can be used (a saving of 13 patients). Interpretation: The approach we describe is especially useful for trials in rare disorders, or for proof-of-concept studies, where it is important to minimise the trial duration and financial costs, particularly in single-arm cancer trials commonly associated with expensive treatment options

Is abdominal drainage after open emergency appendectomy for complicated appendicitis beneficial or waste of money? A single centre retrospective cohort study

BACKGROUND: Appendicitis is a medical condition that causes painful inflammation of the appendix. For acute appendicitis, appendectomy is immediately required as any delay may lead to serious complications such as gangrenous or perforated appendicitis with or without localized abscess formation. Patients who had appendectomy for complicated appendicitis are more prone to develop post-operative complications such as peritoneal abscess or wound infection. Sometimes, abdominal drainage is used to reduce these complications. However, the advantage of the abdominal drainage to minimize post-operative complications is not clear. Therefore, the aim of this study was to investigate whether the use of abdominal drainage after open emergency appendectomy for complicated appendicitis (perforated appendicitis with localized abscess formation only) can prevent or significantly reduce post-operative complications such as intra-peritoneal abscess formation or wound infection. METHODS: In this retrospective cohort study, files and notes were reviewed retrospectively for patients who had open emergency appendectomy for complicated appendicitis (perforated appendicitis with localized abscess formation only) and who had already been admitted and discharged from the surgical wards of Kerbala medical university/Imam Hussein medical city hospital/Kerbala/Iraq. Patients were selected according to specific inclusion and exclusion criteria. Patients were divided into two groups; drainage and non-drainage groups. The drainage group had intra-abdominal drain inserted after the surgery, while the non-drainage group had no drain placed post-operatively. A comparison between both groups was done in terms of these parameters; (i) the development of post operative intra-peritoneal abscess and or wound infection. (ii) The length and cost of hospital stay. (iii) The mortality outcomes. Statistical analysis was done using Pearson Chi-square test, Independent sample t-test and Mann-Whitney U Test. RESULTS: Of 227 patients with open emergency appendectomy for complicated appendicitis, 114 had received abdominal drain after the surgery. Fifty out of 114 patients (43.9%) with abdominal drainage developed post-operative intra-peritoneal abscess (abdominal or pelvic) while 53 out of 113 patients (46.9%) without drainage developed the same complication (P = 0.65). It was also revealed that for patients with drainage, 42 patients (36.8%) had post-operative wound infection, whereas this number was 38 (33.6%) for patients without drainage (P = 0.61). On the other hand, the patients with drain had significantly longer length of hospital stay (mean length of stay: 4.99 days versus 2.12 days, P < 0.001) and significantly higher cost (median cost per patient: $120 versus$60, P < 0.001). CONCLUSION: Installation of abdominal drainage after open emergency appendectomy for complicated appendicitis did not bring any considerable advantage in terms of prevention or significant reduction of post-operative intra-peritoneal abscess and wound infection. Rather, it lengthened the hospital stay and doubled the cost of operation

The planform mobility of river channel confluences: Insights from analysis of remotely sensed imagery

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.River channel confluences are widely acknowledged as important geomorphological nodes that control the downstream routing of water and sediment, and which are locations for the preservation of thick fluvial deposits overlying a basal scour. Despite their importance, there has been little study of the stratigraphic characteristics of river junctions, or the role of confluence morphodynamics in influencing stratigraphic character and preservation potential. As a result, although it is known that confluences can migrate through time, models of confluence geomorphology and sedimentology are usually presented from the perspective that the confluence remains at a fixed location. This is problematic for a number of reasons, not least of which is the continuing debate over whether it is possible to discriminate between scour that has been generated by autocyclic processes (such as confluence scour) and that driven by allocyclic controls (such as sea-level change). This paper investigates the spatial mobility of river confluences by using the 40-year record of Landsat Imagery to elucidate the styles, rates of change and areal extent over which large river confluence scours may migrate. On the basis of these observations, a new classification of the types of confluence scour is proposed and applied to the Amazon and Ganges-Brahmaputra-Meghna (GBM) basins. This analysis demonstrates that the drivers of confluence mobility are broadly the same as those that drive channel change more generally. Thus in the GBM basin, a high sediment supply, large variability in monsoonal driven discharge and easily erodible bank materials result in a catchment where over 80% of large confluences are mobile over this 40-year window; conversely this figure is < 40% for the Amazon basin. These results highlight that: i) the potential areal extent of confluence scours is much greater than previously assumed, with the location of some confluences on the Jamuna (Brahmaputra) River migrating over a distance of 20 times the tributary channel width; ii) extensive migration in the confluence location is more common than currently assumed, and iii) confluence mobility is often tied to the lithological and hydrological characteristics of the drainage basins that determine sediment yield.This work was funded by NERC grant NE/I023228/1 to Sambrook Smith, Bull, Nicholas and Best

The sedimentology of river confluences

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this record.Channel confluences are key nodes within large river networks, and yet surprisingly little is known about their spatial and temporal evolution. Moreover, because confluences are associated with vertical scour that typically extends to several times the mean channel depth, the deposits associated with such scours should have a high preservation potential within the rock record. Paradoxically, such scours are rarely observed, and their preservation and sedimentological interpretation are poorly understood. The present study details results from a physically‐based morphodynamic model that is applied to simulate the evolution and alluvial architecture of large river junctions. Boundary conditions within the model were defined to approximate the junction of the Ganges and Jamuna rivers, Bangladesh, with the model output being supplemented by geophysical datasets collected at this junction. The numerical simulations reveal several distinct styles of sedimentary fill that are related to the morphodynamic behaviour of bars, confluence scour downstream of braid bars, bend scour and major junction scour. Comparison with existing, largely qualitative, conceptual models reveals that none of these can be applied simply, although elements of each are evident in the deposits generated by the numerical simulation and observed in the geophysical data. The characteristics of the simulated scour deposits are found to vary according to the degree of reworking caused by channel migration, a factor not considered adequately in current conceptual models of confluence sedimentology. The alluvial architecture of major junction scours is thus characterized by the prevalence of erosion surfaces in conjunction with the thickest depositional sets. Confluence scour downstream of braid bar and bend scour sites may preserve some large individual sets, but these locations are typically characterized by lower average set thickness compared to major junction scour and by a lack of large‐scale erosional surfaces. Areas of deposition not related to any of the specific scour types highlighted above record the thinnest depositional sets. This variety in the alluvial architecture of scours may go some way towards explaining the paradox of ancient junction scours, that while abundant large scours are likely in the rock record, they have been reported rarely. The present results outline the likely range of confluence sedimentology and will serve as a new tool for recognizing and interpreting these deposits in the ancient fluvial record.This work was funded by a UK Natural Environment Research Council award to Sambrook Smith (NE/I023228/1), Bull (NE/I023864/1) and Nicholas (NE/I023120/1)

One-pot synthesis and negative ion mass spectrometric investigation of a densely functionalized cinnoline, 3-amino-5,7,8-trichloro-6-hydroxycinnoline-4-carbonitrile

Known densely substituted 3-amino-5,7,8-trichloro-6-hydroxycinnoline-4-carbonitrile was synthesized using a new synthetic protocol involving chloranil and malonitrile via quinone methide formation. This one-pot synthesis occurs under base mediated conditions in a polar medium. The method involves condensation of excess malononitrile with chloranil in ethanol at reflux to 2-(2,4,5-trichloro-3-hydroxy-6-oxocyclohexa-2,4-dien-1-ylidene) malononitrile. This is an atom efficient, simple and effective procedure for the preparation of a highly substituted cinnoline that can serve as a relay to antimalarial prototypes

Identification of novel clostridium perfringens type E strains that carry an iota toxin plasmid with a functional enterotoxin gene

Clostridium perfringens enterotoxin (CPE) is a major virulence factor for human gastrointestinal diseases, such as food poisoning and antibiotic associated diarrhea. The CPE-encoding gene (cpe) can be chromosomal or plasmid-borne. Recent development of conventional PCR cpe-genotyping assays makes it possible to identify cpe location (chromosomal or plasmid) in type A isolates. Initial studies for developing cpe genotyping assays indicated that all cpe-positive strains isolated from sickened patients were typable by cpe-genotypes, but surveys of C. perfringens environmental strains or strains from feces of healthy people suggested that this assay might not be useful for some cpe-carrying type A isolates. In the current study, a pulsed-field gel electrophoresis Southern blot assay showed that four cpe-genotype untypable isolates carried their cpe gene on a plasmid of ~65 kb. Complete sequence analysis of the ~65 kb variant cpe-carrying plasmid revealed no intact IS elements and a disrupted cytosine methyltransferase (dcm) gene. More importantly, this plasmid contains a conjugative transfer region, a variant cpe gene and variant iota toxin genes. The toxin genes encoded by this plasmid are expressed based upon the results of RT-PCR assays. The ~65 kb plasmid is closely related to the pCPF4969 cpe plasmid of type A isolates. MLST analyses indicated these isolates belong to a unique cluster of C. perfringens. Overall, these isolates carrying a variant functional cpe gene and iota toxin genes represent unique type E strains. © 2011 Miyamoto et al

Pesticidal Activity of Sundarban Mangrove Plant Extracts against Sitophilus Pests and Identification of Active Constituents Using LC-MS.

Plants act as a rich source of novel natural pesticides. In the backdrop of the recent revival of interest in developing plant-based insecticides, this study was carried out to investigate the pesticidal activity of Sundarban mangrove plants. A total of nine different plant parts from five plants, namely, Aegiceras corniculatum, Excoecaria agallocha, Heritiera fomes, Xylocarpus moluccensis, and Xylocarpus granatum, were extracted with methanol and tested for insecticidal activity against two common stored product pests Sitophilus oryzae and Sitophilus zeamais using direct contact feeding deterrent wafer disc method. Three bark extracts from A. corniculatum, E. agallocha, and H. fomes showed potent and statistically significant insecticidal activity against both S. oryzae and S. zeamais pests (80-100% mortality). All the active bark extracts were further fractionated using C-18 solid-phase extraction (SPE) columns and tested for their insecticidal activity against S. oryzae pest to identify the active fraction. Only the SPE4 fraction (100% MeOH) from all the three active plants showed the activity against S. oryzae pest with a lethal concentration 50% (LC50) value of 0.5, 1.0, and 1.5 mg/disc for A. corniculatum, E. agallocha, and H. fomes, respectively. The active fraction of A. corniculatum was further profiled for identification of active compounds using LC-ESI-MS and identified (along with some unknown peaks) two previously reported compounds at m/z 625.17630 (isorhamnetin 3-O-rutinoside) and 422.25346 (paspaline) as major constituents. Insecticidal activities of these plants are reported in this study for the first time and would be useful in promoting research aiming for the development of new biopesticides from mangrove plants