A Combinatorial Approach to the Variable Selection in Multiple Linear Regression: Analysis of Selwood et al Data set -A Case Study.

A combinatorial protocol (CP) is introduced here to interface it with the multiple linear regression (MLR) for variable selection. The efficiency of CP-MLR is primarily based on the restriction of entry of correlated variables to the model development stage. It has been used for the analysis of Selwood et al data set [16], and the obtained models are compared with those reported from GFA [8] and MUSEUM [9] approaches. For this data set CP-MLR could identify three highly independent models (27, 28 and 31) with Q2 value in the range of 0.632-0.518. Also, these models are divergent and unique. Even though, the present study does not share any models with GFA [8], and MUSEUM [9] results, there are several descriptors common to all these studies, including the present one. Also a simulation is carried out on the same data set to explain the model formation in CP-MLR. The results demonstrate that the proposed method should be able to offer solutions to data sets with 50 to 60 descriptors in reasonable time frame. By carefully selecting the inter-parameter correlation cutoff values in CP-MLR one can identify divergent models and handle data sets larger than the present one without involving excessive computer time.

On the detection of dynamic responses in a drought-perturbed tropical rainforest in Borneo

The dynamics of aseasonal lowland dipterocarp forest in Borneo is influenced by perturbation from droughts. These events might be increasing in frequency and intensity in the future. This paper describes drought-affected dynamics between 1986 and 2001 in Sabah, Malaysia, and considers how it is possible, reliably and accurately, to measure both coarse- and fine-scale responses of the forest. Some fundamental concerns about methodology and data analysis emerge. In two plots forming 8 ha, mortality, recruitment, and stem growth rates of trees ≥10 cm gbh (girth at breast height) were measured in a ‘pre-drought’ period (1986–1996), and in a period (1996–2001) including the 1997–1998 ENSO-drought. For 2.56 ha of subplots, mortality and growth rates of small trees (10–<50 cm gbh) were found also for two sub-periods (1996–1999, 1999–2001). A total of c. 19 K trees were recorded. Mortality rate increased by 25% while both recruitment and relative growth rates increased by 12% for all trees at the coarse scale. For small trees, at the fine scale, mortality increased by 6% and 9% from pre-drought to drought and on to ‘post-drought’ sub-periods. Relative growth rates correspondingly decreased by 38% and increased by 98%. Tree size and topography interacted in a complex manner with between-plot differences. The forest appears to have been sustained by off-setting elevated tree mortality by highly resilient stem growth. This last is seen as the key integrating tree variable which links the external driver (drought causing water stress) and population dynamics recorded as mortality and recruitment. Suitably sound measurements of stem girth, leading to valid growth rates, are needed to understand and model tree dynamic responses to perturbations. The proportion of sound data, however, is in part determined by the drought itself.

Evolution of the leukotoxin promoter in genus Mannheimia

BACKGROUND: The Mannheimia species encompass a wide variety of bacterial lifestyles, including opportunistic pathogens and commensals of the ruminant respiratory tract, commensals of the ovine rumen, and pathogens of the ruminant integument. Here we present a scenario for the evolution of the leukotoxin promoter among representatives of the five species within genus Mannheimia. We also consider how the evolution of the leukotoxin operon fits with the evolution and maintenance of virulence. RESULTS: The alignment of the intergenic regions upstream of the leukotoxin genes showed significant sequence and positional conservation over a 225-bp stretch immediately proximal to the transcriptional start site of the lktC gene among all Mannheimia strains. However, in the course of the Mannheimia genome evolution, the acquisition of individual noncoding regions upstream of the conserved promoter region has occurred. The rate of evolution estimated branch by branch suggests that the conserved promoter may be affected to different extents by the types of natural selection that potentially operate in regulatory regions. Tandem repeats upstream of the core promoter were confined to M. haemolytica with a strong association between the sequence of the repeat units, the number of repeat units per promoter, and the phylogenetic history of this species. CONCLUSION: The mode of evolution of the intergenic regions upstream of the leukotoxin genes appears to be highly dependent on the lifestyle of the bacterium. Transition from avirulence to virulence has occurred at least once in M. haemolytica with some evolutionary success of bovine serotype A1/A6 strains. Our analysis suggests that changes in cis-regulatory systems have contributed to the derived virulence phenotype by allowing phase-variable expression of the leukotoxin protein. We propose models for how phase shifting and the associated virulence could facilitate transmission to the nasopharynx of new hosts.

Expression Analysis of the Theileria parva Subtelomere-Encoded Variable Secreted Protein Gene Family

Background The intracellular protozoan parasite Theileria parva transforms bovine lymphocytes inducing uncontrolled proliferation. Proteins released from the parasite are assumed to contribute to phenotypic changes of the host cell and parasite persistence. With 85 members, genes encoding subtelomeric variable secreted proteins (SVSPs) form the largest gene family in T. parva. The majority of SVSPs contain predicted signal peptides, suggesting secretion into the host cell cytoplasm. Methodology/Principal Findings We analysed SVSP expression in T. parva-transformed cell lines established in vitro by infection of T or B lymphocytes with cloned T. parva parasites. Microarray and quantitative real-time PCR analysis revealed mRNA expression for a wide range of SVSP genes. The pattern of mRNA expression was largely defined by the parasite genotype and not by host background or cell type, and found to be relatively stable in vitro over a period of two months. Interestingly, immunofluorescence analysis carried out on cell lines established from a cloned parasite showed that expression of a single SVSP encoded by TP03_0882 is limited to only a small percentage of parasites. Epitope-tagged TP03_0882 expressed in mammalian cells was found to translocate into the nucleus, a process that could be attributed to two different nuclear localisation signals. Conclusions Our analysis reveals a complex pattern of Theileria SVSP mRNA expression, which depends on the parasite genotype. Whereas in cell lines established from a cloned parasite transcripts can be found corresponding to a wide range of SVSP genes, only a minority of parasites appear to express a particular SVSP protein. The fact that a number of SVSPs contain functional nuclear localisation signals suggests that proteins released from the parasite could contribute to phenotypic changes of the host cell. This initial characterisation will facilitate future studies on the regulation of SVSP gene expression and the potential biological role of these enigmatic proteins.

Diagnostic delay in Crohn's disease is associated with a complicated disease course and increased operation rate

OBJECTIVES The impact of diagnostic delay (a period from appearance of first symptoms to diagnosis) on the clinical course of Crohn's disease (CD) is unknown. We examined whether length of diagnostic delay affects disease outcomes. METHODS Data from the Swiss IBD cohort study were analyzed. Patients were recruited from university centers (68%), regional hospitals (14%), and private practices (18%). The frequencies of occurrence of bowel stenoses, internal fistulas, perianal fistulas, and CD-related surgery (intestinal and perianal) were analyzed. RESULTS A total of 905 CD patients (53.4% female, median age at diagnosis 26 (20-36) years) were stratified into four groups according to the quartiles of diagnostic delay (0-3, 4-9, 10-24, and ≥25 months, respectively). Median diagnostic delay was 9 (3-24) months. The frequency of immunomodulator and/or antitumor necrosis factor drug use did not differ among the four groups. The length of diagnostic delay was positively correlated with the occurrence of bowel stenosis (odds ratio (OR) 1.76, P=0.011 for delay of ≥25 months) and intestinal surgery (OR 1.76, P=0.014 for delay of 10-24 months and OR 2.03, P=0.003 for delay of ≥25 months). Disease duration was positively associated and non-ileal disease location was negatively associated with bowel stenosis (OR 1.07, P<0.001, and OR 0.41, P=0.005, respectively) and intestinal surgery (OR 1.14, P<0.001, and OR 0.23, P<0.001, respectively). CONCLUSIONS The length of diagnostic delay is correlated with an increased risk of bowel stenosis and CD-related intestinal surgery. Efforts should be undertaken to shorten the diagnostic delay.

Intensive Rotational Grazing of Steers at the Andrew Jackson Demonstration Farm

Fifty head of crossbred steers started grazing 51 acres of pasture on May 1 in a rotational grazing system using a variable density paddock system. Twenty-two head grazed 92 days, 27 grazed 140 days, and one steer died. A total of 11,922 pounds was produced on 5,804 animal-days of grazing. The average daily gain was 2.02 pounds for group 1 and 2.07 for group 2. The stocking rate for the first 92 days was .98 steers per acre and .53 for the final 48 days. The animal days of grazing per acre was 113 and the pounds of gain per acre was 233. Total return for land, labor and management for the demonstration was $2,829.76 or $55.49/acre.

Management Intensive Grazing of Stockers at the Andrew Jackson Demonstration Farm (1996 – 1998)

The Andrew Jackson Demonstration Farm (AJDF) is located in central Jackson County in east central Iowa. A board of directors operates the farm for the purpose of demonstrating different production practices and management strategies. From 1996 to 1998 management intensive grazing practices and the grazing of stockers on a combination of permanent and tillable pasture have been demonstrated. Grazing strategies or practices demonstrated during these years included establishment of Eastern Gamagrass and Big Bluestem, variable density grazing, measuring forage on-offer, estimating dry matter intake, grazing corn, pasture renovation, and fencing and water systems. Production performance data were gathered for the three years stockers that were grazed. During this time the stockers averaged 121 animal days of grazing, a 1.1 head per acre stocking rate, a 1.85 pound average daily gain, and 228 pounds of gain per acre. The financial measures evaluated the value of gain on pasture and the pasture cost of the gain. The value of gain per pound was positive for 1996 and 1997 at $.58 and $.52 whereas in 1998 it was a -$.04. Pasture costs per pound of gain ranged from $.12 to $.16. Production performance is only one part of the profit picture when evaluating a stocker operation. Buysell margins are the other significant part that can greatly impact the profit potential of a summer grazing program.

Clinical outcomes following subgingival application of a novel erythritol powder by means of air polishing in supportive periodontal therapy: a randomized, controlled clinical study

OBJECTIVES The aim of this prospective, randomized, controlled clinical study was to compare the clinical outcomes of the subgingival treatment with erythritol powder by means of an air-polishing (EPAP) device and of scaling and root planing (SRP) during supportive periodontal therapy (SPT). METHOD AND MATERIALS 40 patients enrolled in SPT were randomly assigned to two groups of equal size. Sites had to show signs of inflammation (bleeding on probing [BOP]-positive) and a probing pocket depth (PPD) of ≥ 4 mm, however, without presence of detectable subgingival calculus. During SPT, these sites were treated with EPAP or SRP, respectively. Full mouth and site-specific plaque indices, BOP, PPD, and clinical attachment level (CAL) were recorded at baseline (BL) and at 3 months, whereas the percentage of study sites positive for BOP (BOP+) was considered as primary outcome variable. Additionally, patient comfort using a visual analog scale (VAS) and the time needed to treat per site was evaluated. RESULTS At 3 months, mean BOP level measured 45.1% at test sites and 50.6% at control sites, respectively, without a statistically significant difference between the groups (P > .05). PPD and CAL slightly improved for both groups with comparable mean values at 3 months. Evaluation of patient tolerance showed statistically significantly better values among patients receiving the test treatment (mean VAS [0-10], 1.51) compared to SRP (mean VAS [0-10], 3.66; P = .0012). The treatment of test sites was set to 5 seconds per site. The treatment of control sites, on the other hand, lasted 85 seconds on average. CONCLUSION The new erythritol powder applied with an air-polishing device can be considered a promising modality for repeated instrumentation of residual pockets during SPT. CLINICAL RELEVANCE With regard to clinical outcomes during SPT, similar results can be expected irrespective of the two treatment approaches of hand instrumentation or subgingival application of erythritol powder with an air-polishing device in sites where only biofilm removal is required.

Influence of rubber dam on objective and subjective parameters of stress during dental treatment of children and adolescents - a randomized controlled clinical pilot study

BACKGROUND Rubber dam is recommended for isolating the working field during adhesive dentistry procedures; however, dentists often omit rubber dam, particularly in paediatric dentistry, supposing that it would stress the patient. AIM The aim of this study was to evaluate stress parameters during a standardized dental treatment procedure performed with or without rubber dam. The treatment time was measured as a secondary outcome variable. DESIGN This study was designed as a randomized, controlled, clinical study with 72 patients (6-16 years; mean age, 11.1). During standardized fissure sealing procedures, objective parameters of stress (e.g., skin resistance, breath rate) were recorded. The operator's stress level was measured by pulse rate. Subjective pain (patients) and stress perception (operator) were evaluated by an interview. RESULTS The breath rate was significantly (P<0.05) lower and the skin resistance level was significantly higher during treatment with rubber dam compared to the control group. Subjective pain perception was significantly lower for the test group. The treatment time needed for the fissure sealing procedure was 12.4% less in the test group. CONCLUSION Isolation with rubber dam caused less stress in children and adolescents compared to relative isolation with cotton rolls if applied by an experienced dentist.

The effect of monoalkyl phosphates and fluoride on dissolution of hydroxyapatite, and interactions with saliva

The aims were to investigate the effect of monoalkyl phosphates (MAPs) and fluoride on dissolution rate of native and saliva-coated hydroxyapatite (HA). Fluoride at 300 mg/l (as NaF) inhibited dissolution of native HA by 12%, while potassium and sodium dodecyl phosphates (PDP, SDP), at 0.1% or higher, inhibited dissolution by 26-34%. MAPs, but not fluoride, also showed persistence of action. MAPs at 0.5% and fluoride at 300 mg/l were then tested separately against HA pre-treated with human saliva for 2 or 18 h. Agents were applied with brushing to half the specimens, and without brushing to the other half. In control (water-treated) specimens, pre-treatment of HA with human saliva reduced dissolution rate on average by 41% (2 h) and 63% (18 h). Brushing did not have a statistically significant effect on dissolution rate of saliva-coated specimens. In brushed specimens, fluoride significantly increased the inhibition due to 2- or 18-hour saliva pre-treatment. It is hypothesised that brushing partially removes the salivary film and allows KOH-soluble calcium fluoride formation at the surfaces of HA particles. Inhibition was reduced by PDP in 2-hour/non-brushed specimens and in 18-hour/brushed specimens. PDP did not affect dissolution rates in the remaining groups and SDP did not affect dissolution rate in any group. Possible reasons for these variable results are discussed. The experiments show that pre-treatment with saliva can significantly modify results of tests on potential anti-erosive agents and it is recommended that saliva pre-treatment should be a routine part of testing such agents.

NLO thermal dilepton rate at non-zero momentum

The vector channel spectral function and the dilepton production rate from a QCD plasma at a temperature above a few hundred MeV are evaluated up to next-to-leading order (NLO) including their dependence on a non-zero momentum with respect to the heat bath. The invariant mass of the virtual photon is taken to be in the range K2 ~ (πT)2 ~ (1GeV)2, generalizing previous NLO results valid for K2 ≫ (πT)2. In the opposite regime 0 < K2 ≪ (πT)2 the loop expansion breaks down, but agrees nevertheless in order of magnitude with a previous result obtained through resummations. Ways to test the vector spectral function through comparisons with imaginary-time correlators measured on the lattice are discussed.

Thermal right-handed neutrino production rate in the relativistic regime

The production rate of right-handed neutrinos from a Standard Model plasma at a temperature above a hundred GeV is evaluated up to NLO in Standard Model couplings. The results apply in the so-called relativistic regime, referring parametrically to a mass M ~ πT, generalizing thereby previous NLO results which only apply in the non-relativistic regime M ≫ πT. The non-relativistic expansion is observed to converge for M ≳ 15T, but the smallness of any loop corrections allows it to be used in practice already for M ≳ 4T. In the latter regime any non-covariant dependence of the differential rate on the spatial momentum is shown to be mild. The loop expansion breaks down in the ultrarelativistic regime M ≪ πT, but after a simple mass resummation it nevertheless extrapolates reasonably well towards a result obtained previously through complete LPM resummation, apparently confirming a strong enhancement of the rate at high temperatures (which facilitates chemical equilibration). When combined with other ingredients the results may help to improve upon the accuracy of leptogenesis computations operating above the electroweak scale.

Intelligence is related to specific processes in visual change detection: Fixed-links modeling of hit rate and reaction time

By means of fixed-links modeling, the present study identified different processes of visual short-term memory (VSTM) functioning and investigated how these processes are related to intelligence. We conducted an experiment where the participants were presented with a color change detection task. Task complexity was manipulated through varying the number of presented stimuli (set size). We collected hit rate and reaction time (RT) as indicators for the amount of information retained in VSTM and speed of VSTM scanning, respectively. Due to the impurity of these measures, however, the variability in hit rate and RT was assumed to consist not only of genuine variance due to individual differences in VSTM retention and VSTM scanning but also of other, non-experimental portions of variance. Therefore, we identified two qualitatively different types of components for both hit rate and RT: (1) non-experimental components representing processes that remained constant irrespective of set size and (2) experimental components reflecting processes that increased as a function of set size. For RT, intelligence was negatively associated with the non-experimental components, but was unrelated to the experimental components assumed to represent variability in VSTM scanning speed. This finding indicates that individual differences in basic processing speed, rather than in speed of VSTM scanning, differentiates between high- and low-intelligent individuals. For hit rate, the experimental component constituting individual differences in VSTM retention was positively related to intelligence. The non-experimental components of hit rate, representing variability in basal processes, however, were not associated with intelligence. By decomposing VSTM functioning into non-experimental and experimental components, significant associations with intelligence were revealed that otherwise might have been obscured.

The effect of heart rate reduction by ivabradine on collateral function in patients with chronic stable coronary artery disease

Objective To evaluate the effect of heart rate reduction by ivabradine on coronary collateral function in patients with chronic stable coronary artery disease (CAD). Methods This was a prospective randomised placebo-controlled monocentre trial in a university hospital setting. 46 patients with chronic stable CAD received placebo (n=23) or ivabradine (n=23) for the duration of 6 months. The main outcome measure was collateral flow index (CFI) as obtained during a 1 min coronary artery balloon occlusion at study inclusion (baseline) and at the 6-month follow-up examination. CFI is the ratio between simultaneously recorded mean coronary occlusive pressure divided by mean aortic pressure both subtracted by mean central venous pressure. Results During follow-up, heart rate changed by +0.2±7.8 beats/min in the placebo group, and by –8.1±11.6 beats/min in the ivabradine group (p=0.0089). In the placebo group, CFI decreased from 0.140±0.097 at baseline to 0.109±0.067 at follow-up (p=0.12); it increased from 0.107±0.077 at baseline to 0.152±0.090 at follow-up in the ivabradine group (p=0.0461). The difference in CFI between the 6-month follow-up and baseline examination amounted to −0.031±0.090 in the placebo group and to +0.040±0.094 in the ivabradine group (p=0.0113). Conclusions Heart rate reduction by ivabradine appears to have a positive effect on coronary collateral function in patients with chronic stable CAD.