Miracle-dz/UniFAR-FTUs huggingface dataset:
Sensitivity and Specificity Can Change in Opposite Directions When New Predictive Markers Are Added to Risk Models

When comparing prediction models, it is essential to estimate the magnitude of change in performance rather than rely solely on statistical significance. In this paper we investigate measures that estimate change in classification performance, assuming 2-group classification based on a single risk threshold. We study the value of a new biomarker when added to a baseline risk prediction model. First, simulated data are used to investigate the change in sensitivity and specificity (ΔSe and ΔSp). Second, the influence of ΔSe and ΔSp on the net reclassification improvement (NRI; sum of ΔSe and ΔSp) and on decision-analytic measures (net benefit or relative utility) is studied. We assume normal distributions for the predictors and assume correctly specified models such that the extended model has a dominating receiver operating characteristic curve relative to the baseline model. Remarkably, we observe that even when a strong marker is added it is possible that either sensitivity (for thresholds below the event rate) or specificity (for thresholds above the event rate) decreases. In these cases, decision-analytic measures provide more modest support for improved classification than NRI, even though all measures confirm that adding the marker improved classification accuracy. Our results underscore the necessity of reporting ΔSe and ΔSp separately. When a single summary is desired, decision-analytic measures allow for a simple incorporation of the misclassification costs.
Macrolide antibiotics for cystic fibrosis.

BACKGROUND Cystic Fibrosis is characterised by chest infection, the antibiotic treatment of which has significantly improved the outlook for people with this condition. The unusual nature of organisms that infect the chest of individuals with cystic fibrosis has restricted antibiotic choice. In particular the bacteria, Pseudomonas aeruginosa, is resistant to nearly all antibiotics that can be taken by mouth. There is laboratory evidence and evidence from other disease processes that macrolide antibiotics, whilst not directly active against Pseudomonas aeruginosa, may have indirect actions against this bacteria. OBJECTIVES This review aimed to test the hypotheses that macrolide antibiotics; 1) Improve clinical status compared to placebo or another antibiotic 2) do not have unacceptable adverse effects If benefit was demonstrated, we aimed to assess the optimal type, dose and duration of macrolide therapy. SEARCH STRATEGY We searched the Cochrane Cystic Fibrosis and Genetic Disorders Group specialist trials register which comprises references identified from comprehensive electronic database searches, handsearching relevant journals and handsearching abstract books of conference proceedings. In addition, Principal Investigators, known to work in the field and previous authors were contacted for unpublished or follow up data. Pharmaceutical companies, that manufacture macrolide antibiotics, were approached. SELECTION CRITERIA Randomised controlled trials, published or unpublished, of macrolide compared to placebo, another class of antibiotic or another macrolide. Studies which compare regimes of the same macrolide at different doses will also be included. DATA COLLECTION AND ANALYSIS No completed randomised controlled trials were identified. MAIN RESULTS Three open studies excluded. Four ongoing randomised controlled trials were identified. No completed randomised controlled trials were identified. REVIEWER'S CONCLUSIONS At present, there are no randomised controlled trials to evaluate the use of macrolide antibiotics for the treatment of chest infection in people with cystic fibrosis. Such trials, with clear outcome measures, are needed to properly evaluate this potentially useful treatment for cystic fibrosis.
Empirical Examination of Market Reaction to Transfer Pricing Taxation Announcement in Press: A Japanese Perspective ∗

The Japanese Taxation Agency (JTA) introduced transfer pricing taxation (TPT) in order to suppress the outflow of profits and therefore taxes of Japanese companies, which are expanding overseas. There have been many press reports regarding the application of TPT, and so there is much public attention on this issue. TPT is applied to unnatural transfer prices (TP). If TPT is applied to a multinational company (MNC), the company will need to bear enormous documentation costs in its calculation of the ratable price. In addition, in the last few years, the target of TPT is shifting to the overseas transfer of intangible assets, such as trademarks, royalties, patents, and charges income. As a result, companies have become more careful about TPT and investors tend to pay attention to companies’ TPT strategy. With regard to this point, this paper examines how the market evaluates news regarding TP by investigating the market reaction to an initial press report mentioning that a firm was involved in a TP manipulation and may be guilty of tax underpayment. We examine these events both because press reports are currently under intense scrutiny and because there has been very little research on firms that engage in tax sheltering (see, e.g., Graham & Tucker, 2006; Hanlon & Slemrod, 2009). Some view the fact that not all firms engage in tax sheltering as surprising because of the widespread view that shelters, at least in the 1990s, in expectation, offered a positive net present value position. The potential negative public relations effect is often cited as one reason for this “under-sheltering” phenomenon (Bankman, 2004). On the event study analysis, we find that the Japanese capital market has shown a statistically significant negative reaction to the press reports. This result is due to a strong distrust of corporate activity regarding TP strategies. Moreover, in order to clarify the reason why the market responds to reports of TPT being applied, we compute the cumulative abnormal returns (CARs) around the date of the press report and conduct two-stage least-squares estimation to examine where this result regarding the market reaction comes from. Our results indicate that the variables for intangible assets and effective tax rate and the variables which represent the extent of corporate governance (CG) are statistically significant with respect to these reactions.
Fast multislice mapping of the myelin water fraction using multicompartment analysis of T  2* decay at 3T: A preliminary postmortem study

Quantitative mapping of the myelin water content can provide significant insight into the pathophysiology of several white matter diseases, such as multiple sclerosis and leukoencephalopathies, and can potentially become a useful clinical tool for early diagnosis of these diseases. In this study, multicompartment analysis of T 2* decay (MCAT2*) was used for the quantitative mapping of myelin water fraction (MWF). T 2* decay of each voxel at multiple slice locations was acquired in fixed human brains using a multigradient‐echo (MGRE) pulse sequence with alternating readout gradient polarities. Compared to prior techniques using Carr‐Purcell‐Meiboom‐Gill (CPMG) acquisition, the MGRE acquisition approach has: 1) a very short first echo time (≈2 ms) and echo‐spacing (≈1 ms), which allows for the acquisition of multiple sampling points during the fast decay of the myelin water signal; 2) a low RF duty cycle, which is especially important for achieving acceptable specific absorption rate (SAR) levels at high field strengths. Multicompartment analysis was then applied to the T 2* decay in each pixel using a 3‐pool model of white matter to detect the signal arising from the myelin water, myelinated axonal water, and mixed water compartments. Magn Reson Med 58:865–870, 2007. © 2007 Wiley‐Liss, Inc.
Killing of tumor cells in vitro by macrophages from mice treated with synthetic dehydrodipeptides.

Treatment of NMRI mice i.p. with dehydrodipeptides [acetyldehydro-3-(2-thienyl)alanyltyrosine (SI); acetyldehydro-3-(2-furyl)alanyltyrosine (SII)] rendered macrophages cytolytic for several tumor cells in vitro. Normal peritoneal mouse macrophages from untreated mice not given injections of the peptides or from control mice given injections of phosphate-buffered saline were not cytotoxic. Moreover, supernatants from these in vivo-activated mouse peritoneal macrophages significantly increased the release of the cytoplasmic enzyme lactate dehydrogenase from freshly added target cells, showing that these cells had been killed. The macrophage activation to lyse tumor cells was sharply dose dependent and appeared about 48 hr after injection of the peptides. Although dehydrodipeptide SI was active in vivo at concentrations as low as 500 microgram/mouse, the same substance lacked activity in vitro at all concentrations tested up to 800 microgram/ml. Dehydrodipeptides activate macrophages through a T-cell-independent process to lyse tumor target cells. Macrophages from athymic nude (nu/nu) mice were less cytotoxic, but they still were stimulated; and the culture supernatants could kill about 50% of the tumor cells used. There are indications for a relative specific structure-activity relationship of dehydrodipeptides for inducing cytotoxic macrophages.
Susceptibility of wild mouse cells to exogenous infection with xenotropic leukemia viruses: control by a single dominant locus on chromosome 1

Although xenotropic murine leukemia viruses cannot productively infect cells of laboratory mice, cells from various wild-derived mice can support replication of these viruses. Although the virus-sensitive wild mice generally lack all or most of the xenotropic proviral genes characteristic of inbred strains, susceptibility to exogenous infection is unrelated to inheritance of these sequences. Instead, susceptibility is controlled by a single dominant gene, designated Sxv, which maps to chromosome 1. Sxv is closely linked to, but distinct from Bxv-1, the major locus for induction of xenotropic murine leukemia viruses in laboratory mice. Genetic experiments designed to characterize Sxv show that this gene also controls sensitivity to a wild mouse virus with the interference properties of mink cell focus-forming murine leukemia viruses, and that Sxv-mediated susceptibility to xenotropic murine leukemia viruses is restricted by the mink cell focus-forming virus resistance gene Rmcf. These data, together with genetic mapping of the mink cell focus-forming virus cell surface receptor locus to this same region of chromosome 1, suggest that Sxv may encode a wild mouse variant of the mink cell focus-forming virus receptor that allows penetration by xenotropic murine leukemia viruses.
Income inequalities in the Polish subregions and their implications for the well-being of inhabitants

The neoclassic economic model assumes that individual’s utility level depends on individual’s or her family’s absolute income. Homo economicus does not compare his income with the income of others. However, number of recent studies suggest the existence of a negative impact of income inequality on the level of subjective well-being. Using the data from Social Diagnosis 2011 the paper aims at measuring the relation of income inequalities in Polish subregions and the level subjective well-being of their inhabitants. The results of the study are not conclusive and do not provide strong arguments either for rejecting or accepting the hypothesis of the negative effect of social inequalities in subregions on subjective well-being.
ANALISIS MONDAY EFFECT DAN ROGALSKI EFFECT DI BURSA EFEK JAKARTA

Penelitian ini bertujuan untuk menguji pengaruh hari perdagangan di Bursa Efek Indonesia dengan menggunakan 70 saham yang aktif di perdagangkan selama periode penelitian 2004-2006. Teknik sampling menggunakan purposive sampling dengan kriteria sampel adalah saham-saham yang aktif diperdagangkan selama periode penelitian. Pengujian hipotesis menggunakan regresi dengan variable dummy. Hasil penelitian mengindikasikan bahwa ada pengaruh hari perdagangan terhadap return saham di Bursa Efek Indonesia. Return tertinggi terjadi pada hari Jumat dan return terendah pada hari Senin. Dengan hasil tersebut, dapat dikatakan penelitian ini berhasil mengidentifikasi adanya Monday effect dan weekend effect. Pengujian Rogalski effect menunjukkan bahwa Rogalski effect terjadi pada bulan April. The paper investigates the day of the week effect in Indonesia Stock Exchange by using 70 active stocks during the period of 2004-2006. Sampling technique uses purposive sampling and the criteria of the sample is stocks which are trading actively during the period of study. Regression with dummy variables are use to test the hypothesis. The findings indicate that there is a day of the week effect in Indonesia Stock exchange, the highest returns are observed on Friday and the lowest returns are observed on Monday. It can be said that this study can identify Monday effect and weekend effect in Jakarta Stock Exchange. The Investigation about Rogalski effect in JSX find that Rogalski effect presents in April. Monday’s return being positive in April and remain negative in the other months, so Monday effect disappeared in April.
catena-Poly[[{N,N-dimethyl-N′-[1-(pyridin-2-yl)ethylidene]ethane-1,2-diamine-κ3 N,N′,N′′}(thiocyanato-κN)cadmium]-μ-thiocyanato-κ2 S:N]

In the title compound, [Cd(NCS)2(C11H17N3)]n, the CdII atom is octahedrally coordinated by the N,N′,N′′-tridentate Schiff base ligand and one terminal thiocyanate N atom. Two trans-N:S-bridging thiocyanates complete the N5S donor set around the Cd atom. In the crystal, adjacent CdII ions are linked by the thiocyanate N:S-bridges into polymeric chains along the c axis.
Recommendations for immunizations in stem cell transplantation

Abstract: Investigations over the past decade have documented that there is a decline in immunity to vaccine preventable diseases in many SCT recipients. The majority of immunization studies conducted in SCT recipients to date support the use of multi‐dose regimens for most protein and polysaccharide‐conjugate vaccine antigens. The consensus immunization schedule recommended by ACIP/IDSA/ASBMT provides guidance for centers to utilize available vaccines in their SCT populations. With the exception of pneumococcal disease, a schedule beginning at 12 months after SCT is reasonable given the low incidence of disease in HSCT recipients for most of the recommended vaccines and improved immune reconstitution in most recipients by one year post transplant. SCT recipients respond poorly to unconjugated pneumococcal polysaccharide vaccine and the development of polysaccharide‐protein conjugate vaccines against S. pneumoniae holds promise to impact potentially on clinical disease in this population. In addition, the strategy of donor immunization may also be effective in eliciting early protective immune responses to vaccine antigens. Future challenges will be the development of safe and effective vaccines against the viral pathogens responsible for considerable morbidity and mortality after SCT.
Metabolic and Transcriptomic Adaptation of Lactococcus lactis subsp. lactis Biovar diacetylactis in Response to Autoacidification and Temperature Downshift in Skim Milk

ABSTRACT For the first time, a combined genome-wide transcriptome and metabolic analysis was performed with a dairy Lactococcus lactis subsp. lactis biovar diacetylactis strain under dynamic conditions similar to the conditions encountered during the cheese-making process. A culture was grown in skim milk in an anaerobic environment without pH regulation and with a controlled temperature downshift. Fermentation kinetics, as well as central metabolism enzyme activities, were determined throughout the culture. Based on the enzymatic analysis, a type of glycolytic control was postulated, which was shared by most of the enzymes during the growth phase; in particular, the phosphofructokinase and some enzymes of the phosphoglycerate pathway during the postacidification phase were implicated. These conclusions were reinforced by whole-genome transcriptomic data. First, limited enzyme activities relative to the carbon flux were measured for most of the glycolytic enzymes; second, transcripts and enzyme activities exhibited similar changes during the culture; and third, genes involved in alternative metabolic pathways derived from some glycolytic metabolites were induced just upstream of the postulated glycolytic bottlenecks, as a consequence of accumulation of these metabolites. Other transcriptional responses to autoacidification and a decrease in temperature were induced at the end of the growth phase and were partially maintained during the stationary phase. If specific responses to acid and cold stresses were identified, this exhaustive analysis also enabled induction of unexpected pathways to be shown.
The (sub-)millimeter SED of protoplanetary disks in the outskirts of the Orion nebula cluster

We present the sub-mm/mm SED for a sample of eight young circumstellar disks in the outer regions of the Orion nebula cluster (ONC). New observations were carried out at 2.9 mm with the CARMA array and for one disk, 216-0939, at 3.3 and 6.8 mm with ATCA. By combining these new millimeter data with literature measurements at sub-millimeter wavelengths we investigate grain growth and measure the dust mass in protoplanetary disks in the ONC. These data provide evidence for dust grain growth to at least millimeter-sizes for the first time in a high-mass star-forming region. The obtained range in sub-mm/mm spectral index, namely 1.5–3.2, indicates that for disks in the outskirts of the ONC (projected distance from the cluster center between about 0.4 pc and 1.5 pc) grain growth to mm sizes occurs in the same manner as disks in regions where only low-mass stars form. Finally, in our sample three disks are more massive than about 0.05 M_⊙, confirming that massive disks are present in the outer regions of the Orion nebula.
Safety and efficacy of cold polypectomy compared to endoscopic mucosal resection and hot biopsy polypectomy

Abstract Backgrounds: Recently, several studies have demonstrated the usefulness of cold polypectomy (CP), a safe and simple method for the removal of small polyps. We investigated the safety and efficacy of CP compared to that of endoscopic mucosal resection (EMR) and hot biopsy polypectomy (HB). Methods: We retrospectively examined 1713 colorectal polyps (size 1–9 mm) in 731 patients. CP, EMR, and HB were performed on 476, 997, and 240 lesions, respectively. We compared the region, size, morphology, the presence of delayed bleeding as overt bleeding 24 h after operation, number of clips, pathology, the presence of antithrombotic therapy, procedure time from detection of a polyp to resection and hemostasis, device cost including device and clips, and polyp remnants. Results: The delayed bleeding in the CP group (0/476) was significantly lower compared to that in the HB group (3/240) and EMR group (7/997). There were no cases of perforations. The procedure time was significantly shorter in the CP group than in the EMR group (91.3sec vs 290.1sec, p < .0001). The CP group had a significantly lower device cost than the HB and EMR groups (49.2USD vs 58.0 USD vs 91.3 USD, p < .0001) was not inferior in terms of polyp remnants to the EMR and HB groups. (1.4% vs 0.6% vs 6.1%, p = .1599) Conclusions: CP is a safe treatment that achieves less delayed bleeding. Moreover, CP is not inferior to other groups in terms of polyp remnants and offers a cost benefit. CP can be considered useful for colonic polypectomy.
Adaptive Tasks, Coping and Quality of Life of Chronically Ill Patients

This article is a report of a larger study on the relationship between adaptive tasks, coping and quality of life, taking Parkinson's disease and chronic fatigue syndrome (CFS) as examples. The concept of adaptive tasks or disease-related stressors testing the adaptive capacities of chronically ill patients (N=134) was explored by applying the method of concept mapping. Results show that patients both with Parkinson's disease and with CFS generally refer to the same themes when asked for the adaptive tasks their disease brings about. However, the actual contents of these adaptive tasks differ as well as their impact on coping and quality of life. In the case of patients with Parkinson's disease, objective disease characteristics appear to be more important in predicting quality of life than in the case of patients with CFS, whose evaluation of adaptive tasks is predictive of quality of life.
Low job control and risk of coronary heart disease in whitehall ii (prospective cohort) study

Abstract Objective: To determine the association between adverse psychosocial characteristics at work and risk of coronary heart disease among male and female civil servants. Design: Prospective cohort study (Whitehall II study). At the baseline examination (1985-8) and twice during follow up a self report questionnaire provided information on psychosocial factors of the work environment and coronary heart disease. Independent assessments of the work environment were obtained from personnel managers at baseline. Mean length of follow up was 5.3 years. Setting: London based office staff in 20 civil service departments. Subjects: 10 308 civil servants aged 35-55 were examined-6895 men (67%) and 3413 women (33%). Main outcome measures: New cases of angina (Rose questionnaire), severe pain across the chest, diagnosed ischaemic heart disease, and any coronary event. Results: Men and women with low job control, either self reported or independently assessed, had a higher risk of newly reported coronary heart disease during follow up. Job control assessed on two occasions three years apart, although intercorrelated, had cumulative effects on newly reported disease. Subjects with low job control on both occasions had an odds ratio for any subsequent coronary event of 1.93 (95% confidence interval 1.34 to 2.77) compared with subjects with high job control at both occasions. This association could not be explained by employment grade, negative affectivity, or classic coronary risk factors. Job demands and social support at work were not related to the risk of coronary heart disease. Conclusions: Low control in the work environment is associated with an increased risk of future coronary heart disease among men and women employed in government offices. The cumulative effect of low job control assessed on two occasions indicates that giving employees more variety in tasks and a stronger say in decisions about work may decrease the risk of coronary heart disease. Key messages Low job control in the work environment contributes to the development of coronary heart disease among British male and female civil servants The risk of heart disease is associated with both objective low job control and perceived low job control. Increase in job control over time decreases the risk of coronary heart disease. This suggests that policies giving people a stronger say in decisions about their work or providing them with more variety in work tasks may contribute to better cardiovascular health