Miracle-dz/UniFAR-FTUs huggingface dataset:
On damage, uncertainty and risk in supervised control: aphids and brown rust in winter wheat as an example.

In supervised control of pests and diseases real-time information on pest and disease intensity and cost-benefit analysis of decision alternatives are used to support farmers' decisions on pesticide application. This thesis focuses on improving supervised control in the pathosystem aphids - brown rust - winter wheat. First, effects of the grain aphid, Sitobion avenae , on crop physiology are studied to arrive at simple relations between aphid density and damage. Second, the consequences of uncertainty about the costs of alternative strategies for optimal timing of chemical control of aphids and/or brown rust ( Pucciniarecondita ) are evaluated. Uptake of assimilates by S. avenae and reduction of the rate of net leaf photosynthesis by honeydew were quantified and introduced into a model which simulates growth and development of winter wheat from flowering till ripeness. Attainable yields from 4000 to 10000 kg ha -1and damage at the higher yield levels were simulated satisfactorily. Honeydew caused more damage than assimilate uptake at crop development stages until milky ripeness. Attainable yield, crop development stage, and timing and intensity of infestation were of major importance in explaining variation in damage. The results of the simulation model were summarized in regression models which predicted damage at given infestation levels as good as the best published empirical model. Sources of uncertainty in a decision model for evaluating costs of chemical control strategies were quantified using field data. Assessment of the contribution of various sources of uncertainty to model output uncertainty showed white noise in the relative growth rates of both aphids and brown rust to be the major cause of uncertainty. Risk-neutral damage thresholds representing pest intensities at which expected costs of control just exceed expected costs of no control, were considerably lower than the deterministic damage thresholds based on average input values. At the risk-neutral damage thresholds only 30% of chemical applications was found to be cost-effective. To support pest control under uncertainty a framework is proposed in which alternative strategies are evaluated in terms of 'profitability' and 'risk', operational measures of the economic objectives 'return on investment' and 'insurance', respectively.
Anterior Cingulate Cortex and Response Conflict : Effects of Response Modality and Processing Domain

posterior to the genu and superior to the corpus callosum. However, it is not clear whether the same ACC region is activated for all response modalities (e.g. vocal and manual) and/or all processing domains (e.g. verbal and spatial). To explore this question, we used rapid event-related functional magnetic resonance imaging and a spatial Stroop task with conditions tapping both verbal and spatial processing. We also employed novel methods that allowed us to acquire the accuracy and reaction times of both manual and vocal responses. We found one large ACC region that demonstrated significant response conflict effects with both vocal and manual responses, and three ACC regions that demonstrated significant response conflict effects with both spatial and verbal processing. We did not find any ACC regions that demonstrated activity selective to either a specific response modality or processing domain. Thus, our results suggest that the same regions of ACC are responsive to conflict arising with both manual and vocal output and with both spatial and verbal processing.
Meta-analysis of individual patient data versus aggregate data from longitudinal clinical trials

Background In clinical trials following individuals over a period of time, the same assessment may be made at a number of time points during the course of the trial. Our review of current practice for handling longitudinal data in Cochrane systematic reviews shows that the most frequently used approach is to ignore the correlation between repeated observations and to conduct separate meta-analyses at each of a number of time points. Purpose The purpose of this paper is to show the link between repeated measurement models used with aggregate data and those used when individual patient data (IPD) are available, and provide guidance on the methods that practitioners might use for aggregate data meta-analyses, depending on the type of data available. Methods We discuss models for the meta-analysis of longitudinal continuous outcome data when IPD are available. In these models time is included either as a factor or as a continuous variable, and account is taken of the correlation between repeated observations. The meta-analysis of IPD can be conducted using either a one-step or a two-step approach: the latter involves analysing the IPD separately in each study and then combining the study estimates taking into account their covariance structure. We discuss the link between models for use with aggregate data and the two-step IPD approach, and the problems which arise when only aggregate data are available. The methods are applied to IPD from 5 trials in Alzheimer's disease. Results Two major issues for the meta-analysis of aggregate data are the lack of information about correlation coefficients and the effect of missing data at the patient-level. Application to the Alzheimer's disease data set shows that ignoring correlation can lead to different pooled estimates of the treatment difference and their standard errors. Furthermore, the amount of missing data at the patient level can affect these estimates. Limitations The models assume fixed treatment effects across studies, and that any missing data is missing at random, both at the patient-level and the study level. Conclusions It is preferable to obtain IPD from all studies to correctly account for the correlation between repeated observations. When IPD are not available, the ideal aggregate data are model-based estimates of treatment difference and their variance and covariance estimates. If covariance estimates are not available, sensitivity analyses should be undertaken to investigate the robustness of the results to different amounts of correlation. Clinical Trials 2009; 6: 16—27. http:// ctj.sagepub. com
Peptidoglycan Induces the Production of Interleukin-8 via Calcium Signaling in Human Gingival Epithelium

The etiology of periodontal disease is multifactorial. Exogenous stimuli such as bacterial pathogens can interact with toll-like receptors to activate intracellular calcium signaling in gingival epithelium and other tissues. The triggering of calcium signaling induces the secretion of pro-inflammatory cytokines such as interleukin-8 as part of the inflammatory response; however, the exact mechanism of calcium signaling induced by bacterial toxins when gingival epithelial cells are exposed to pathogens is unclear. Here, we investigate calcium signaling induced by bacteria and expression of inflammatory cytokines in human gingival epithelial cells. We found that peptidoglycan, a constituent of gram-positive bacteria and an agonist of toll-like receptor 2, increases intracellular calcium in a concentration-dependent manner. Peptidoglycan-induced calcium signaling was abolished by treatment with blockers of phospholipase C (U73122), inositol 1,4,5-trisphosphate receptors, indicating the release of calcium from intracellular calcium stores. Peptidoglycan-mediated interleukin-8 expression was blocked by U73122 and 1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetrakis (acetoxymethyl ester). Moreover, interleukin-8 expression was induced by thapsigargin, a selective inhibitor of the sarco/endoplasmic reticulum calcium ATPase, when thapsigargin was treated alone or co-treated with peptidoglycan. These results suggest that the gram-positive bacterial toxin peptidoglycan induces calcium signaling via the phospholipase C/inositol 1,4,5-trisphosphate pathway, and that increased interleukin-8 expression is mediated by intracellular calcium levels in human gingival epithelial cells.
Parameter optimization of awavelet-based electrocardiogram delineator with an evolutionary algorithm

A recurrent problem encountered in many algorithms proposed to detect and segment ECG waves is the adjustment of the numerous parameters used. This work presents a method to optimize these parameters with an evolutionary algorithm (EA). The signal processing chain contains a filter to remove baseline wandering, a QRS detector (Pan & Tompkins) and a wave segmentation step based on the wavelet-transform (WT). The EA adjusts the parameters of the segmentation step in order to minimize the result of a cost function which measures how close the detector is from characteristic points annotated by a cardiologist. Results obtained with the QTDB are compared with other approaches of wave segmentation for which thresholds have been experimentally defined. EAs have shown to be an effective method to solve this complex problem of multiobjective optimization
Increased risk of atherothrombotic events associated with cytochrome P450 3A5 polymorphism in patients taking clopidogrel

Background: Clopidogrel is a prodrug requiring metabolism by cytochrome P450 3A (CYP3A) isoenzymes, including CYP3A5, in order to be active. It is controversial whether clopidogrel interacts with CYP3A inhibitors. We investigated the influence of CYP3A5 polymorphism on the drug interaction of clopidogrel. Methods: In phase 1 of the study, we administered clopidogrel to 16 healthy volunteers who had the CYP3A5 non-expressor genotype (*3 allele) and 16 who had the CYP3A5 expressor genotype (*1 allele) with and without pretreatment with itraconazole, a potent CYP3A inhibitor. A platelet aggregation test was performed at baseline, 4 hours, 24 hours and 6 days after clopidogrel administration. In phase 2, we compared clinical outcomes of 348 patients treated with clopidogrel after successful coronary angioplasty with bare-metal stent implantation according to their CYP3A5 genotype; the primary end point was a composite of atherothrombotic events (cardiovascular death, myocardial infarction and non-hemorrhagic stroke) within 1 and 6 months after stent implantation. Results: In phase 1, the change in platelet aggregation after clopidogrel administration and pretreatment with itraconazole was greater among the subjects with the CYP3A5 expressor genotype than among those with the non-expressor genotype: 24.9% (standard deviation [SD] 13.9%) v. 6.2% (SD 13.5%) at 4 hours (p < 0.001); 27.7% (SD 16.5%) v. 2.5% (SD 8.3%) at 24 hours (p < 0.001); and 33.5% (SD 18.6%) v. 17.8% (SD 13.8%) at day 7 (p < 0.01). In phase 2, atherothrombotic events occurred more frequently within 6 months after stent implantation among the patients with the non-expressor genotype than among those with the expressor genotype (14/193 v. 3/155; p = 0.023). Multivariable analysis showed that the CYP3A5 polymorphism was a predictor of atherothrombotic events in clopidogrel users. Interpretation: People with the CYP3A5 non-expressor genotype are vulnerable to drug interactions between clopidogrel and CYP3A inhibitors. This phenomenon may be associated with worse outcomes in patients with the non-expressor genotype who are given clopidogrel after coronary angioplasty and implantation of bare-metal stents.
URBAN PARK AND FOREST PARTICIPATION AND LANDSCAPE PREFERENCE: A COMPARISON BETWEEN BLACKS AND WHITES IN PHILADELPHIA AND ATLANTA, U.S.

Previous research has documented the existence of differences in the attitudes and behaviors of Blacks and Whites in American society toward urban parks and forest areas. However, many of these studies were carried out a decade or more ago and/or most focused on specific parks or localized areas. Data from a recent survey of residents in two metropolitan areas in the eastern United States allowed for updating of this research record. Using analysis of variance and covariance, consideration was given to racial differences between Blacks and Whites, regional differences between cities, and the effects of various socio-demographic characteristics on residents’ park preferences and participation. Racial differences were similar to those reported by previous researchers, and these differences did not vary markedly between the two metropolitan study sites. These distinctions, combined with racial differences in subjects’ expressed willingness to volunteer time to develop/maintain local park settings, suggest the importance of understanding the differing perspectives and actions of multi-ethnic user groups in urban park and forest management and maintenance.
Clinical utility of antimicrobial susceptibility measurement plate covering formulated concentrations of various ophthalmic antimicrobial drugs

Purpose The purpose of this study was to evaluate the clinical utility of SG17, an ophthalmic antimicrobial susceptibility measurement plate. Design This was a multicenter, retrospective, observational study. Patients and methods Using clinical isolates from patients with ocular infections, drug susceptibility testing using the Clinical Laboratory and Standards Institute standards was routinely conducted at five facilities. The minimum inhibitory concentrations of the isolated strains were determined using SG17 at the Research Foundation for Microbial Diseases of Osaka University. The records of antimicrobial drugs used and the therapeutic course were evaluated for all cases. The susceptibility results from SG17 and routine methods used at each facility were compared. Results A total of 112 bacterial strains were isolated from 92 patients. Of these cases, keratitis was the most common (52.2%), followed by conjunctivitis (21.7%) and others (26.1%). Principal signs and symptoms resolved in all patients, indicating that therapeutic effects had been achieved. With SG17, drug susceptibility was determined in 98.9% of isolates compared with 30.4% of isolates determined using conventional methods. By adapting the Clinical Laboratory and Standards Institute standards to SG17 results, we found that 91.3% of patients were susceptible and 7.6% were resistant. In five patients, drugs with a resistant evaluation were initially administered with no effect, and the patients were then switched to drugs with a susceptible evaluation with final resolution, indicating agreement of clinical results with SG17. Conclusion SG17 can be used to determine drug susceptibility to antimicrobial agents currently used in ophthalmic practice. SG17 is useful for selecting antimicrobial drugs.
A flow‐condition‐based interpolation finite element procedure for triangular grids

A flow‐condition‐based interpolation finite element scheme is presented for use of triangular grids in the solution of the incompressible Navier–Stokes equations. The method provides spatially isotropic discretizations for low and high Reynolds number flows. Various example solutions are given to illustrate the capabilities of the procedure. This article replaces a previously published version, which was retracted due to printing errors: International Journal for Numerical Methods in Fluids 2005; 49(8):849–875 [DOI: 10.1002/fld.1027]. Retraction notice DOI: 10.1002/fld.1247 Copyright © 2006 John Wiley & Sons, Ltd.
Nickel chloride (NiCl2)-caused inflammatory responses via activation of NF-κB pathway and reduction of anti-inflammatory mediator expression in the kidney

Nickel (Ni) or Ni compounds target a number of organs and produce multiple toxic effects. Kidney is the major organ for Ni accumulation and excretion. There are no investigations on the Ni- or Ni compounds-induced renal inflammatory responses in human beings and animals at present. Therefore, we determined NiCl2-caused alteration of inflammatory mediators, and functional damage in the broiler's kidney by the methods of biochemistry, immunohistochemistry and quantitative real-time polymerase chain reaction (qRT-PCR). Dietary NiCl2 in excess of 300 mg/kg caused the renal inflammatory responses that characterized by increasing mRNA expression levels of the pro-inflammatory mediators including tumor necrosis factor-α (TNF-α), cyclooxygenase-2 (COX-2), interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8) and interleukin-18 (IL-18) via the activation of nucleic factor κB (NF-κB), and decreasing mRNA expression levels of the anti-inflammatory mediators including interleukin-2 (IL-2), interleukin-4 (IL-4) and interleukin-13 (IL-13). Concurrently, NiCl2 caused degeneration, necrosis and apoptosis of the tubular cells, which was consistent with the alteration of renal function parameters including elevated alkaline phosphatase (AKP) activity, and reduced activities of sodium-potassium adenosine triphosphatase (Na+/K+-ATPase), calcium adenosine triphosphatase (Ca2+-ATPase), lactic dehydrogenase (LDH), succinate dehydrogenase (SDH) and acid phosphatase (ACP) in the kidney. The above-mentioned results present that the activation of NF-κB pathway and reduction of anti-inflammatory mediator expression are main mechanisms of NiCl2-caused renal inflammatory responses and that the renal function is decreased or impaired after NiCl2-treated.
In situ mantle cell lymphoma: clinical implications of an incidental finding with indolent clinical behavior

Background Cyclin D1-positive B cells are occasionally found in the mantle zones of reactive lymphoid follicles, a condition that has been called “in situ mantle cell lymphoma”. The clinical significance of this lesion remains uncertain. Design and Methods The clinical and pathological characteristics, including SOX11 expression, of 23 cases initially diagnosed as in situ mantle cell lymphoma were studied. Results Seventeen of the 23 cases fulfilled the criteria for in situ mantle cell lymphoma. In most cases, the lesions were incidental findings in reactive lymph nodes. The t(11;14) was detected in all eight cases examined. SOX11 was positive in seven of 16 cases (44%). Five cases were associated with other small B-cell lymphomas. In two cases, both SOX11-positive, the in situ mantle cell lymphoma lesions were discovered after the diagnosis of overt lymphoma; one 4 years earlier, and one 3 years later. Twelve of the remaining 15 patients had a follow-up of at least 1 year (median 2 years; range, 1–19.5), of whom 11 showed no evidence of progression, including seven who were not treated. Only one of 12 patients with an in situ mantle cell lymphoma lesion and no diagnosis of mantle cell lymphoma at the time developed an overt lymphoma, 4 years later; this case was also SOX11-positive. The six remaining cases were diagnosed as mantle cell lymphoma with a mantle zone pattern. Five were SOX11-positive and four of them were associated with lymphoma without a mantle zone pattern. Conclusions In situ mantle cell lymphoma lesions are usually an incidental finding with a very indolent behavior. These cases must be distinguished from mantle cell lymphoma with a mantle zone pattern and overt mantle cell lymphoma because they may not require therapeutic intervention.
A New Species of Stream Frog (Sanguirana) from the Mountains of Luzon Island, Philippines

Abstract: We describe a distinctively patterned new species of cascade stream frog from the mountains of Nueva Vizcaya and Aurora provinces, Luzon Island. The new species belongs to the genus Sanguirana, the definition of which we expand to include all Philippine species previously referred to the Rana (Hylarana) everetti complex. The new species is distinguished from other members of the genus by its possession of a bright yellow-green dorsum with conspicuous orange flower-shaped spots in females, bright white, postaxial dermal flanges on the limbs, green-to-purple flank transition, and a highly tuberculate, white venter, in addition to the absence of a dark canthal stripe. The new species is known only from high-gradient, cascading mountain streams between elevations of 750 and 1450 m in mature secondary forest and minimally disturbed primary forests. The discovery of such a distinctive new species emphasizes the relatively high degree to which endemic anuran diversity in the Philippines is still underestimated and underappreciated.
Transforming into an elementary technology specialist: Stories of change

The experiences of elementary technology integration specialists in a Midwestern school district were explored through narrative case studies as these educators transitioned from classroom teaching to roles as technology integration specialists. Four specialists participated in the study, two who had recently assumed this position (novices), and two who served in the specialist role for more than ten years (experienced). Including novice and experienced participants allowed the researcher to elicit narratives relative to current as well as historical perceptions of the processes that affected decisions to pursue a role as a technology integration specialist role. Experienced participants’ narratives were explored to uncover perceptions of ways in which their professional identities have changed over time. A mixed methods research design was employed. The primary design was qualitative: case studies incorporated the results of semi-structured interviews as well as teaching observations. Over a five-week period, each participant engaged in a cycle of setting weekly instructional goals (referred to as a “mindset checklist”) and post-instruction journaling about their experiences, then setting new and/or revised instructional goals. These goals were used to construct personalized observation protocols, used by the researcher as the basis for teaching observations. Interview transcripts were analyzed using the constant comparative method. Quantitative elements were incorporated to provide additional information relative to participants’ self-theories of ability (mindset) and self-efficacy pertaining to instructional technology. Analyses revealed a key technology beliefs pattern: participants who expressed (through their narratives) and subsequently demonstrated (during instructional observations) the belief that their technology integration knowledge and skills would improve through sustained effort scored higher on a quantitative technology perseverance assessment, and also demonstrated greater perseverance while teaching when they
The distribution of faults in a large industrial software system

A case study is presented using thirteen releases of a large industrial inventory tracking system. Several types of questions are addressed in this study. The first involved examining how faults are distributed over the different files. This included making a distinction between the release during which they were discovered, the lifecycle stage at which they were first detected, and the severity of the fault. The second category of questions we considered involved studying how the size of modules affected their fault density. This included looking at questions like whether or not files with high fault densities at early stages of the lifecycle also had high fault densities during later stages. A third type of question we considered was whether files that contained large numbers of faults during early stages of development, also had large numbers of faults during later stages, and whether faultiness persisted from release to release. Finally, we examined whether newly written files were more fault-prone than ones that were written for earlier releases of the product. The ultimate goal of this study is to help identify characteristics of files that can be used as predictors of fault-proneness, thereby helping organizations determine how best to use their testing resources.