Quantifying selective reporting and the Proteus phenomenon for multiple datasets with similar bias

Meta-analyses play an important role in synthesizing evidence from diverse studies and datasets that address similar questions. A major obstacle for meta-analyses arises from biases in reporting. In particular, it is speculated that findings which do not achieve formal statistical significance are less likely reported than statistically significant findings. Moreover, the patterns of bias can be complex and may also depend on the timing of the research results and their relationship with previously published work. In this paper, we present an approach that is specifically designed to analyze large-scale datasets on published results. Such datasets are currently emerging in diverse research fields, particularly in molecular medicine. We use our approach to investigate a dataset on Alzheimer's disease (AD) that covers 1167 results from case-control studies on 102 genetic markers. We observe that initial studies on a genetic marker tend to be substantially more biased than subsequent replications. The chances for initial, statistically non-significant results to be published are estimated to be about 44% (95% CI, 32% to 63%) relative to statistically significant results, while statistically non-significant replications have almost the same chance to be published as statistically significant replications (84%; 95% CI, 66% to 107%). Early replications tend to be biased against initial findings, an observation previously termed Proteus phenomenon: The chances for non-significant studies going in the same direction as the initial result are estimated to be lower than the chances for non-significant studies opposing the initial result (73%; 95% CI, 55% to 96%). Such dynamic patterns in bias are difficult to capture by conventional methods, where typically simple publication bias is assumed to operate. Our approach captures and corrects for complex dynamic patterns of bias, and thereby helps generating conclusions from published results that are more robust against the presence of different coexisting types of selective reporting.     

Characterization and prediction of protein nucleolar localization sequences

Although the nucleolar localization of proteins is often believed to be mediated primarily by non-specific retention to core nucleolar components, many examples of short nucleolar targeting sequences have been reported in recent years. In this article, 46 human nucleolar localization sequences (NoLSs) were collated from the literature and subjected to statistical analysis. Of the residues in these NoLSs 48% are basic, whereas 99% of the residues are predicted to be solvent-accessible with 42% in α-helix and 57% in coil. The sequence and predicted protein secondary structure of the 46 NoLSs were used to train an artificial neural network to identify NoLSs. At a true positive rate of 54%, the predictor’s overall false positive rate (FPR) is estimated to be 1.52%, which can be broken down to FPRs of 0.26% for randomly chosen cytoplasmic sequences, 0.80% for randomly chosen nucleoplasmic sequences and 12% for nuclear localization signals. The predictor was used to predict NoLSs in the complete human proteome and 10 of the highest scoring previously unknown NoLSs were experimentally confirmed. NoLSs are a prevalent type of targeting motif that is distinct from nuclear localization signals and that can be computationally predicted.     

Person-to-person transmission of Giardia lamblia in day-care nurseries.

In an outbreak of giardiasis at two day-care nurseries in metropolitan Toranto Giardia lamblia appeared to be transmitted person to person. No common source of infection could be found. The proportions of children infected in the two nurseries were 39% and 17%; infection was spread to 7% and 23% of their household contacts. Of the infected children and household contacts 26% and 30% respectively of those for whom detailed information could be obtained were symptomatic. Canadian children were more likely to be infected and symptomatic than were immigrant children attending the nurseries. The most susceptible ages for infection were 1 to 3 years. The results of this study suggest that all children in day-care nurseries who are infected with G. lamblia should be treated, regardless of whether they are symptomatic.     

The Staining of Brunner's Gland and Other Neutral Mucins by Carmine,Hematoxylin and Orcein in Alkaline Solutions

Brunner's glands and other neutral mucins may be stained red, brownish red, and violet, respectively, by carmine, hematoxylin, and orcein from appropriate alkaline solutions. Carmine and hematoxylin in concentrations of 0.2-1% are dissolved in 60-70% alcohol containing 1% potassium carbonate; orein is used in a 0.2% alcoholic solution of sodium hydroxide. Staining times are 15 to 30 minutes. The stained sections are rinsed in 95% or absolute alcohol prior to xylene and mounting. The staining of these mucins is blocked by mild bromine oxidation. By using alcian blue 0.1% in 3% acetic acid for 5 minutes prior to the above stains, mucins may be characterized in the same preparation as acid, neutral or mixed.     

Treatment of wastewater from abattoirs before land application--a review

Pre-treatments are screening, catch basins, flotation, equalization, and settlers for recovering proteins and fats from abattoir wastewater. With chemical addition, dissolved air flotation (DAF) units can achieve chemical oxygen demand (COD) reductions ranging from 32% to 90% and are capable of removing large amounts of nutrients. Aerobic trickling towers reduced soluble COD by additional 27% but did not reduced total COD. Chemical-DAF reduced 67% of total COD and soluble COD. About 40-60% of the solids or approximately 25-35% of the biological oxygen demand (BOD) load can be separated by pre-treatment screening and sedimentation. Anaerobic systems are lagoon, anaerobic contact (AC), up-flow anaerobic sludge blanket (UASB), anaerobic sequence batch reactor (ASBR), and anaerobic filter (AF) processes. Abattoir wastewater is well suited to anaerobic treatment because it is high in organic compounds. Typical reductions of up to 97% BOD, 95% SS and 96% COD are reported. UASB's average COD removal efficiencies are of 80-85%. UASB seems to be a suitable process for the treatment of abattoir wastewater, due to its ability to maintain a sufficient amount of viable sludge. Wastewater in abattoirs can be reduced by treatment of immersion chiller effluent by membrane filtration which can produce recyclable water. Total organic C can be reduced below 100mg/L, and bacteria can not pass through the membrane pores. The abattoir waste minimization options are also discussed.     

The Staining of Brunner's Gland and Other Neutral Mucins by Carmine, Hematoxylin and Orcein in Alkaline Solutions

Brunner's glands and other neutral mucins may be stained red, brownish red, and violet, respectively, by carmine, hematoxylin, and orcein from appropriate alkaline solutions. Carmine and hematoxylin in concentrations of 0.2-1% are dissolved in 60-70% alcohol containing 1% potassium carbonate; orein is used in a 0.2% alcoholic solution of sodium hydroxide. Staining times are 15 to 30 minutes. The stained sections are rinsed in 95% or absolute alcohol prior to xylene and mounting. The staining of these mucins is blocked by mild bromine oxidation. By using alcian blue 0.1% in 3% acetic acid for 5 minutes prior to the above stains, mucins may be characterized in the same preparation as acid, neutral or mixed.     

Arabidopsis plasma membrane proteomics identifies components of transport, signal transduction and membrane trafficking

In order to identify integral proteins and peripheral proteins associated with the plasma membrane, highly purified Arabidopsis plasma membranes from green tissue (leaves and petioles) were analyzed by mass spectrometry. Plasma membranes were isolated by aqueous two-phase partitioning, which yields plasma membrane vesicles with a cytoplasmic-side-in orientation and with a purity of 95%. These vesicles were turned inside-out by treatment with Brij 58 to remove soluble contaminating proteins enclosed in the vesicles and to remove loosely bound contaminating proteins. In total, 238 putative plasma membrane proteins were identified, of which 114 are predicted to have transmembrane domains or to be glycosyl phosphatidylinositol anchored. About two-thirds of the identified integral proteins have not previously been shown to be plasma membrane proteins. Of the 238 identified proteins, 76% could be classified according to function. Major classes are proteins involved in transport (17%), signal transduction (16%), membrane trafficking (9%) and stress responses (9%). Almost a quarter of the proteins identified in the present study are functionally unclassified and more than half of these are predicted to be integral.     

The staining of Brunner's gland and other neutral mucins by carmine, hematoxylin and orcein in alkaline solutions.

Brunner's glands and other neutral mucins may be stained red, brownish red, and violet, respectively, by carmine, hematoxylin, and orcein from appropriate alkaline solutions. Carmine and hematoxylin in concentrations of 0.2-1% are dissolved in 60-70% alcohol containing 1% potassium carbonate; orcein is used in a 0.2% alcoholic solution of sodium hydroxide. Staining times are 15 to 30 minutes. The stained sections are rinsed in 95% or absolute alcohol prior to xylene and mounting. The staining of these mucins is blocked by mild bromine oxidation. By using alcian blue 0.1% in 3% acetic acid for 5 minutes prior to the above stains, mucins may be characterized in the same preparation as acid, neutral or mixed.     

Preliminary survey of Capillaria hepatica (Bancroft, 1893) in Malaysia.

The prevalence of Capillaria hepatica (Bancroft, 1893) infection in a total of 2324 rats trapped from 25 localities in West Malaysia was 15.5%. Infection rates in males (16.0%) and females (15.1%) are similar. A significantly higher percentage of adults (18.1%) than young (7.7%) was infected. Capillaria hepatica infection rates among urban (0.7%) and jungle (0.0%) rats was very low as compared to field rats (17.7%) trapped from agricultural areas such as oil palm estates and rice growing areas. Prevalence of C. hepatica infection in rats is not evenly distributed throughout West Malaysia. There seem to be localised foci of infection. In some areas as many as 77.8% of the adult rats are found to be infected while in other areas the same species of rats are found free of infection.     

Biogeography of the octocorallian coelenterate fauna of southern Africa

The geographical and bathymetric distribution of southern African octocorals is analysed. Of the over 200 estimated species of regional octocorals, 81 confirmed and adequately described species are studied using a radial sector method. Two primary faunal components are recognized–endemic (53.3% of the fauna by numbers of species) and Indo-Pacific (39.4%). An Atlantic component contributes only minimally (about 1.7%), while the remaining fauna is made up of cosmopolites (2.8%) and scattered species (2.8%). A subantarctic component is not evident for the present-day, although evidence for previous contact is presented. A sister-group analysis using genera as a guide to sister species, shows the biogeographic affinities for the present-day fauna as a whole to be 45% Indo-Pacific, 31% cosmopolitan, 10% endemic, 10% Atlantic and 4% southern oceans (subantarctic). Applying the same method to only those genera with endemic species shows the affinities of the present-day endemic fauna to be 27.5% Indo-Pacific, 27.5% endemic, 24% cosmopolitan, 14% Atlantic and 7% subantarctic. Clearly defined boundaries for west, south, and east coast faunas (as recognized by previous authors in describing various intertidal faunas) are found not be present with regard to the octocoral fauna (largely due to its overwhelmingly subtidal nature). Instead two primary zoogeographic provinces are recognized–the Cape Endemic Province (extending from Liideritz to Inhaca Island) and the south-western fringe of the Indo-Pacific Province from East London north-eastwards. An overlap zone between these two is recognized between East London and Inhaca Island, with the region in the vicinity of Richards Bay having an essentially evenly mixed fauna (roughly 50% Cape Endemic Province and 50% Indo-Pacific). Of the 84 octocoral genera recorded for the region, seven (or 8.3%) are endemic, and of these, five are monotypic while two are ditypic. The fauna is shown to be predominantly sublittoral (about 95% by numbers of species), the shallow sublittoral (< 100 m in depth) being the region with highest species richness. Pennatulaceans are eurybathic (intertidal to 4756 m) and clearly show a high proportion of cosmopolites (20% of presently identified species). Soft corals are stenobathic and restricted to the intertidal, continental shelf and uppermost portion of the continental slope (<500m), while gorgonians are intermediate in depth distributon (intertidal to 1200 m). No cosmopolitan alcyonaceans are presently recorded. The centre of the Cape Endemic Province is the Agulhas Bank–an extensive region of shallow continential shelf (< 200 m in depth) between Cape Town and East London. Two regions of octocoral radiation for southern Africa are postulated–the Agulhas Bank and the western Indian Ocean.     

颅骨测量与X线头影测量方法的比较研究

本文对传统的颅骨测量法与口腔医学上使用的X线头影测量法在测量标志点的选取定位及测量结果的差异方面进行了对比研究。测量标志点重叠对比显示颅骨测量中的大多数标志点在X线片上可以较为准确地定位。方差分析表明两种测量方法测量结果差异不显著(P>0.05)。本文就如何准确地在X线片上确定标志点以及测量数据的放大误差问题进行了讨论并提出了将放大率划分为三个等级计算X线头影片测量值的标准。作者认为采用X线头影测量方法进行人类学研究有着良好的应用前景。     

云南省小黑山自然保护区兰科植物多样性及保护评价

云南省小黑山自然保护区孕育了丰富的兰科植物。据调查,保护区有兰科植物43属、134种,约占云南省135属、780种的31.9%和17.2%,是保护区种子植物种类最多的科。兰科植物在保护区的各个生态类型中均有出现。保护区134种兰科植物以附生兰占优势,占67.16%(90种);其次,地生兰占31.34%(42种),腐生兰为1.50%(2种)。保护区兰科植物起源于新、旧世界的热带和温带,热带属占70.0%(28),温带属占27.5%(11)。鉴于兰科植物重要的保护价值,应加强保护区兰科植物的保护。首先应加强保护区的建设和管理,还应加强社区经济发展,加强科学研究,实施社区共管以及加大保护宣传力度。     

Holoprosencephaly

Cardiac tumours are benign or malignant neoplasms arising primarily in the inner lining, muscle layer, or the surrounding pericardium of the heart. They can be primary or metastatic. Primary cardiac tumours are rare in paediatric practice with a prevalence of 0.0017 to 0.28 in autopsy series. In contrast, the incidence of cardiac tumours during foetal life has been reported to be approximately 0.14%. The vast majority of primary cardiac tumours in children are benign, whilst approximately 10% are malignant. Secondary malignant tumours are 10–20 times more prevalent than primary malignant tumours. Rhabdomyoma is the most common cardiac tumour during foetal life and childhood. It accounts for more than 60% of all primary cardiac tumours. The frequency and type of cardiac tumours in adults differ from those in children with 75% being benign and 25% being malignant. Myxomas are the most common primary tumours in adults constituting 40% of benign tumours. Sarcomas make up 75% of malignant cardiac masses. Echocardiography, Computing Tomography (CT) and Magnetic Resonance Imaging (MRI) of the heart are the main non-invasive diagnostic tools. Cardiac catheterisation is seldom necessary. Tumour biopsy with histological assessment remains the gold standard for confirmation of the diagnosis. Surgical resection of primary cardiac tumours should be considered to relieve symptoms and mechanical obstruction to blood flow. The outcome of surgical resection in symptomatic, non-myxomatous benign cardiac tumours is favourable. Patients with primary cardiac malignancies may benefit from palliative surgery but this approach should not be recommended for patients with metastatic cardiac tumours. Surgery, chemotherapy and radiotherapy may prolong survival. The prognosis for malignant primary cardiac tumours is generally extremely poor.     

A system to reproduce and quantify the biomechanical environment of the cell

An in vitro system that permits application of a uniform biomechanical stimulus to a population of cells with great precision has been developed. The device is designed to subject living cells to reproducible and quantifiable biaxial strains from 0 to 10% at rates from quasi-static to 1 s-1 and frequencies from 0 to 5 Hz. Equations for determining the strain in the substrate upon which the cells are grown, based on easily measured parameters, are derived and validated experimentally. The mechanical properties of the substrate are determined, and it is demonstrated that cells can easily be cultured in the apparatus. By use of the system, cloned bovine pulmonary artery endothelial cell clones are subjected to 5% biaxial strains applied at a peak strain rate of 0.5 s-1 and a frequency of 1 Hz for 7 h with cell viability greater than 84% and cell detachment less than 8%. We demonstrate that cells must be attached to the substrate for them to be stretched and that cell strain and substrate strain are not equal. With the use of fluorescently labeled beads as cell surface markers to measure the actual strain produced in the cells as a result of the deformation of the substrate, cell elongation was found to be approximately 60% of the strain in the substrate. This constant appeared to be affected by both in vitro cell age and morphology.     

Demonstration of the Ground Substance of Cartilage, Bone, and Teeth

A slab of bone about 5 mm. thick is decalcified in 5% HCl, washed, and placed for several days to 2-3 weeks in 3% KOH in 20% glycerin (if the bone is medium sized); for small bones the KOH should be decreased to 1%, and for large bones it may be increased to 5%. The solution is changed frequently. When the bone begins to dissociate, it should be removed and washed in water till all traces of alkali are removed. The specimen is passed through 3 changes of dioxane into paraffin, and then through a second paraffin bath into the final paraffin. Sections are cut at 10-12 μ and stained with VanGieson's picro-fuchsin or with orcein.     

A discounted least squares quadratic growth prediction model for use in 2 year toxicity studies.

Weekly weighings of the laboratory rats are required to determine the correct dosage for mixing in the food. This creates problems in that the food mixing must be done immediately after the weighings and staff are often heavily taxed to perform the task. A discounted least squares growth prediction model allows for prediction of weights a week ahead of time, obviating the necessity for instantaneously processing the weight data. When dosages were prepared based on these predictions, for 10 treatment combinations 100% of the doses proved to be within 8-0% of the required dosage; 98-4% were within 5% of the required dosage; 78-7% were within 2% of the required dosage; and 51-6% were within 1% of the required dosage. The quadratic weight prediction model can also be incorporated into a model for predicting food consumption.     

Histochemical Use of Sodium Bismuthate

Histochemical 1,2-glycoI cleavage, similar to that obtained with periodic acid and lead tetraacetate, may be obtained with sodium bismuthate. Routinely prepared slide sections, from tissues fixed in 10% formalin, are run down through xylene and graded alcohols to water and then oxidized for three minutes in a 1% sodium bismuthate 20% aqueous phosphoric acid solution. The oxidizing solution must be freshly prepared and used immediately. Following oxidation, sections are rinsed 15 sec. in IN HC1 to remove bismuth pentoxide precipitate, a by-product of the reaction. The sections are then washed in distilled water and placed in leuco-fushsin for 10 min., or in a saturated 30%) alcoholic solution of p-nitrophenylhydrazine for 5 min. or 2,4-dinitrophenylhydrazine for 30 minutes. After staining, the sections are rinsed in 30% alcohol if the nitrophenylhydrazines were used, or in the standard dilute sulfite bath followed by running tap water for 5 min. if leucofuchsin were used. Sections are routinely dehydrated, cleared, and covered. On examination, the sites of 1,2-glycol linkages will be stained violet by leucofushsin or yellow by the nitrophenylhydrazines.     

DIFFERENTIAL PRESERVATION OF PROTOPLASM IN FOSSIL ANGIOSPERM LEAF TISSUES

Examination of Miocene angiosperm leaf compressions from the Clarkia and Succor Creek localities of Idaho and Oregon reveals a characteristic and predictable pattern of protoplasmic deterioration. Remnants of chloroplasts are preserved in 63.9% of the 8,800 randomly selected cells, while mitochondria (18.6%) and nuclei (11.3%) are less commonly preserved. This pattern appears to be independent of the presumed environment of deposition associated with fossilization. Leaf tissues from sediments thought to be derived from shallow and deeper waters of the Miocene Clarkia lake (Chloro = 34.6%, Mito < 3%, Nuc < 1% and Chloro = 90.1%, Mito = 26%, Nuc = 4.3%, respectively) show similar patterns of ultrastructural preservation to leaves preserved in volcanic ash-fall deposits (Chloro = 80%, Mito = 45.4%, Nuc = 39.5%). Analyses of the data for the relative abundance of various organelles per cell (e.g., in living plants Chloro/Nuc = 250) in fossil tissues and referable modern taxa indicate that the chances of the observed preferential degradation of nuclei being the results of chance is <0.001. The data are interpreted to be evidence for the preferential preservation of chloroplasts and degeneration of nuclei. The pattern of protoplasmic degeneration, reconstructed from the frequencies of organelle preservation, is in contrast to that of the pattern observed in modern plant cell necrosis or senescence where nuclei are the most stable organelle and persist until the death of the cell. Preliminary data indicate that regimes of dehydration and compression may duplicate the pattern of protoplasmic degeneration observed in fossil plant cells.     

Unequivocal determination of sire allele origin for multiallelic microsatellites when only the sire and progeny are genotyped

The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the ‘granddaughter design’. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.     

Double Embedding Again

A method of double embedding fixed tissues in 3% low viscosity nitrocellulose and paraffin is described. Five percent phenol in 80% alcohol during dehydration and 5% glycerin in the nitrocellulose solutions enhance cutting qualities. A modified Ruyter's solution is used to flatten sections. After a section is aflixed to a slide, it is passed through chloroform and acetone to remove the paraftin and celloidin. A 1% celloidin dip insures adherence of the seaion to the slide. Slides are stored in 70% alcohol until they are to be stained. Following staining and dehydration in graded alcohols, clearing should be done in a 1: 3 mixture of terpineol and toluene.