Miracle-dz/UniFAR-FTUs huggingface dataset:
Net risk reclassification p values: valid or misleading?

BACKGROUND The Net Reclassification Index (NRI) and its P value are used to make conclusions about improvements in prediction performance gained by adding a set of biomarkers to an existing risk prediction model. Although proposed only 5 years ago, the NRI has gained enormous traction in the risk prediction literature. Concerns have recently been raised about the statistical validity of the NRI. METHODS Using a population dataset of 10000 individuals with an event rate of 10.2%, in which four biomarkers have no predictive ability, we repeatedly simulated studies and calculated the chance that the NRI statistic provides a positive statistically significant result. Subjects for training data (n = 420) and test data (n = 420 or 840) were randomly selected from the population, and corresponding NRI statistics and P values were calculated. For comparison, the change in the area under the receiver operating characteristic curve and likelihood ratio statistics were calculated. RESULTS We found that rates of false-positive conclusions based on the NRI statistic were unacceptably high, being 63.0% in the training datasets and 18.8% to 34.4% in the test datasets. False-positive conclusions were rare when using the change in the area under the curve and occurred at the expected rate of approximately 5.0% with the likelihood ratio statistic. CONCLUSIONS Conclusions about biomarker performance that are based primarily on a statistically significant NRI statistic should be treated with skepticism. Use of NRI P values in scientific reporting should be halted.
Growth references for 0–19 year-old Norwegian children for length/height, weight, body mass index and head circumference

Background: Previous growth references for Norwegian children were based on measurements from the 1970s and 1980s. New reference data, collected through the Bergen Growth Study and the Medical Birth Registry of Norway, are presented as LMS values. Materials and methods: A cross-sectional sample of children aged 0–19 years in stratified randomized design measured in 2003–2006 as a part of the Bergen Growth Study (n = 7291) and birth data of children born in 1999–2003 from the Medical Birth Registry of Norway (n = 12 576) was used to estimate the new references by the means of the LMS method. Measurement reliability was assessed by test-rest studies. Results: New references were constructed for length/height, weight, body mass index (BMI) and head circumference. Length/height and weight for children aged 0–4 years were similar to previous Norwegian references, but mean height increased up to a maximum of 3.4 cm in boys and 2.5 cm in girls during the pubertal years. Mean height was similar to (or slightly higher) in comparison with other recent European references. Reliability of the measurements compared well with published estimates. Conclusion: Because of the observed secular trends in growth, it is advised to use the new references, which have been endorsed by the Norwegian Department of Health.
A Measurement of Overlap Rate Between Gaussiancomponents

Overlapping clusters often appear in cluster analysis in the data mining. However, the phenomenon of cluster overlapping is still not mathematically well characterized, especially in multivariate cases. In this paper, we are interested in the overlap phenomenon between Gaussian clusters, since the Gaussian mixture is a fundamental data distribution model suitable for many clustering algorithms. We introduce the novel concept of the ridge curve and establish a theory on the degree of overlap between two components. Based on this theory, we develop an algorithm for calculating the overlap rate. We investigate factors that affect the value of the overlap rate, and show how the theory can be used to generate "truthed data" as well as to measure the overlap rate between a given pair of clusters or components in a mixture.
Generation of Eupnea and Sighs by a Spatiochemically Organized Inspiratory Network

The discovery of the rhythmogenic pre-Bötzinger complex (preBötC) inspiratory network, which remains active in a transverse brainstem slice, greatly increased the understanding of neural respiratory control. However, basic questions remain unanswered such as (1) What are the necessary and sufficient slice boundaries for a functional preBötC? (2) Is the minimal preBötC capable of reconfiguring between inspiratory-related patterns (e.g., fictive eupnea and sighs)? (3) How is preBötC activity affected by surrounding structures? Using newborn rat slices with systematically varied dimensions in physiological [K+] (3 mm), we found that a 175 μm thickness is sufficient for generating inspiratory-related rhythms. In 700-μm-thick slices with unilaterally exposed preBötC, a kernel <100 μm thick, centered 0.5 mm caudal to the facial nucleus, is necessary for rhythm generation. Slices containing this kernel plus caudal structures produced eupneic bursts of regular amplitude, whereas this kernel plus rostral tissue generated sighs, intermingled with eupneic bursts of variable amplitude (“eupnea–sigh pattern”). After spontaneous arrest of rhythm, substance-P or neurokinin-1 (NK1) receptor agonist induced the eupnea–sigh burst pattern in ≥250-μm-thick slices, whereas thyrotropin-releasing hormone or phosphodiesterase-4 blockers evoked the eupnea burst pattern. Endogenous rhythm was depressed by NK1 receptor antagonism. Multineuronal Ca2+ imaging revealed that preBötC neurons reconfigure between eupnea and eupnea–sigh burst patterns. We hypothesize a (gradient-like) spatiochemical organization of regions adjacent to the preBötC, such that a small preBötC inspiratory-related oscillator generates eupnea under the dominant influence of caudal structures or thyrotropin-releasing hormone-like transmitters but eupnea–sigh activity when the influence of rostral structures or substance-P-like transmitters predominates.
Hedonic Price Analysis: A View of the Wine Industry in Kentucky

Many world-famous wine zones have been estimated through hedonic price method. Indeed, some objective attributes like grape varieties, vintage are significant in many former works. However, it is still necessary to continue to use this method to study in different regions because there are many reginal-unique attributes. Unlike most previous studies build in wine developed regions, this paper determines the local retail price influence from objective and subjective attributes of wine by estimating hedonic price functions in a wine developing region-Kentucky. Due to most local producers do not have world-wide reputation (or national reputation), it is difficult to figure the ranking effect from those wine celebrities which could be an important attribute variable to determine prices. The hedonic model need to be re-designed by those local attribute variables. The empirical result indicates wines made by single red vitis vinifera are 23.5% higher in retail price than American blend style wine. Compared to the LexingtonFrankfort area, prices of Louisville based wines are 11.8% cheaper and the price discount is 15% for West Kentucky. Compared to dry wines, off dry wines, semisweet wines, and sweet wines are associated with a discount of 16%, 20%, and 13%, respectively in their recommended retail price. A medal of some award adds 12.7% value to the retail wine price holding all other factors constant. For unique local attributes, bourbon barrels used to age wine adds 15% to the price compared to other aging vessels. Finally, holding other factors constant and on average, wine produced in dry counties is 8% cheaper than wine produced in wet counties.
Prevalence and factors associated with irritable bowel syndrome among university students in Lebanon: findings from a cross-sectional study.

AIM To describe the bowel habits and the prevalence of irritable bowel syndrome (IBS) and to investigate the influence of health behavior and social factors on IBS prevalence in university students. METHODS This cross-sectional study was conducted at five major universities in Greater Beirut and its suburbs, between February and June 2014. Using a convenience sample, a total of 813 students aged 18 years old and above participated in this study. Participants were asked to complete a comprehensive anonymous questionnaire which detailed characteristics on socio-demographic, health-related, and lifestyle factors, as well as IBS. The ROME III criteria were used as a tool to ascertain IBS. A χ(2) test was used to determine differences between categorical variables; stepwise logistic regression was used to measure the association between IBS and its risk factors. RESULTS An overall prevalence of IBS of 20% was recorded among university students. The bivariate analysis showed that females were significantly more likely to report having IBS than males (29.1% vs 18.2%, P < 0.01). Those living at the school dormitory or in a private residence (39.5%) were more likely to have IBS than those living with their families (16.3%) (P < 0.01). The multivariate analysis showed that those who had a relatively high family income level (US$ > 2000) were almost 6 times more likely to report having IBS than their counterparts. CONCLUSION This is the first study to describe the nature of IBS among young adults in Lebanon. The prevalence of IBS among university students in our sample was higher than that reported in the West.
Measuring the Performance of Anesthetic Depth Indicators

Background An appropriate measure of performance is needed to identify anesthetic depth indicators that are promising for use in clinical monitoring. To avoid misleading results, the measure must take into account both desired indicator performance and the nature of available performance data. Ideally, anesthetic depth indicator value should correlate perfectly with anesthetic depth along a lighter‐deeper anesthesia continuum. Experimentally, however, a candidate anesthetic depth indicator is judged against a "gold standard" indicator that provides only quantal observations of anesthetic depth. The standard anesthetic depth indicator is the patient's response to a specified stimulus. The resulting observed anesthetic depth scale may consist only of patient "response" versus "no response," or it may have multiple levels. The measurement scales for both the candidate anesthetic depth indicator and observed anesthetic depth are no more than ordinal; that is, only the relative rankings of values on these scales are meaningful. Methods Criteria were established for a measure of anesthetic depth indicator performance and the performance measure that best met these criteria was found. Results The performance measure recommended by the authors is prediction probability PK, a rescaled variant of Kim's dy *symbol* x measure of association. This performance measure shows the correlation between anesthetic depth indicator value and observed anesthetic depth, taking into account both desired performance and the limitations of the data. Prediction probability has a value of 1 when the indicator predicts observed anesthetic depth perfectly, and a value of 0.5 when the indicator predicts no better than a 50:50 chance. Prediction probability avoids the shortcomings of other measures. For example, as a nonparametric measure, PK is independent of scale units and does not require knowledge of underlying distributions or efforts to linearize or to otherwise transform scales. Furthermore, PK can be computed for any degree of coarseness or fineness of the scales for anesthetic depth indicator value and observed anesthetic depth; thus, PK fully uses the available data without imposing additional arbitrary constraints, such as the dichotomization of either scale. And finally, PK can be used to perform both grouped‐ and paired‐data statistical comparisons of anesthetic depth indicator performance. Data for comparing depth indicators, however, must be gathered via the same response‐to‐stimulus test procedure and over the same distribution of anesthetic depths. Conclusions Prediction probability PK is an appropriate measure for evaluating and comparing the performance of anesthetic depth indicators.
Understanding the decision rules for 3D printing adoption

ABSTRACT While 3D printing is a radically different manufacturing method based on advanced technologies, it has not been adopted to-date with as much alacrity as was originally expected. A variety of hidden rules may influence the broad adoption of this novel technology. The purpose of this study is to explore the decision rules for 3D printing adoption from an organisational perspective. Hybrid approaches are proposed to integrate the technology-organisation-environment (TOE) framework and the rough set theory (RST) in order to generate the decision rule and the determinants for 3D printing adoption. An empirical study on manufacturing enterprises in Taiwan is subsequently carried out, with the results revealing a considerable amount of meaningful information that may therefore be useful in the context of management.
A tool based on the co-occurrence matrix to measure the performance of dynamic range reduction algorithms

Recent years have seen an increasing interest in the acquisition of scenes that have a dynamic range far greater than that of conventional acquisition devices. Some software methods have been devised to build high dynamic range (HDR) images by multi-exposure. HDR sensors have also recently appeared. On the other hand, common visualization devices still have a dynamic range that is much lower. A number of software methods have been proposed in the literature to reduce the dynamics of HDR pictures in order to fit low dynamic range displays, while preserving visual information. Usually the performance of these techniques is judged on the basis of visual results. A tool is needed for qualitative and quantitative evaluation. Common evaluation tools lack flexibility, since either they cannot express relevant features, such as local contrast (e.g. histograms), or they are little expressive for qualitative and visual evaluation (e.g. functions that measure contrast). We present a comprehensive tool, based on the co-occurrence matrix, that allows to measure many useful features and can be conveniently used for visual evaluation. We show its expressiveness examining the results of different techniques for dynamic range reduction.
Measuring banking efficiency in Vietnam: parametric and non-parametric methods

The article aims to evaluate the business efficiency of commercial banks in Vietnam using both parametric and non-parametric approaches. In this study, the Stochastic Frontier Analysis (SFA), which belongs to a parametric method, and Data Envelopment Analysis (DEA), a non-parametric approach, are applied to a sample of 30 joint stock commercial banks in Vietnam in the period of 2011–2015. Applying Tobit regression model, the impact of bank size, bank age, and the ownership feature on the efficiency of bank service industry in Vietnam is also investigated. The analysis results show that in general, the Vietnamese banking efficiency is improving during the selected period regardless of techniques used. However, there is small level of similarity in efficiency rankings identified from the SFA and DEA models. In terms of efficiency determinants, the results show that all three variables of size, age, and state ownership have a positive impact on bank efficiency.
Translation initiation factor a/eIF2(-γ) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus

The trimeric translation initiation factor a/eIF2 of the crenarchaeon Sulfolobus solfataricus is pivotal for binding of initiator tRNA to the ribosome. Here, we present in vitro and in vivo evidence that the a/eIF2 γ-subunit exhibits an additional function with resemblance to the eukaryotic cap-complex. It binds to the 5′-triphosphate end of mRNA and protects the 5′ part from degradation. This unprecedented capacity of the archaeal initiation factor further indicates that 5′ → 3′ directional mRNA decay is a pathway common to all domains of life.
The Malmö Food Study: the reproducibility of a novel diet history method and an extensive food frequency questionnaire.

OBJECTIVE To assess the reproducibility of two diet assessment methods, an extensive quantitative food frequency questionnaire (method A) and a novel shorter quantitative food frequency questionnaire with a 14 day food record (method B). DESIGN A randomized prospective cohort study. SETTING General community. SUBJECTS 241 residents of the town of Malmö, aged between 50-69 years, 126 men and 115 women who completed the methods one year apart. METHODS Both diet methods were designed to cover the whole diet and portion sizes were estimated using a booklet with 120 photographs; method A comprised 250 items and method B combined a two-week food record measuring lunch and dinner meals and a shorter 130 item quantitative food frequency questionnaire for average consumption of foods, snacks and beverages during the past year; RESULTS The percent difference between estimated energy intake one year apart were for men 10.7% for method A and 0.2% for method B, corresponding values for women 13.7% and 1.1%. Method B showed a good agreement between measurements for energy-providing nutrients, micronutrients and major food groups, i.e. meat products, edible fats, milk, fish, fruits and vegetables with correlation coefficients between 0.70-0.90 for women. The percent difference of average intake of edible fat was about 10%. Average energy-adjusted Pearson's correlation coefficients were of the order of 0.50-0.80 for most nutrients including 14 fatty acids. The correlation for the ratio between polyunsaturated and saturated fatty acids were about 0.70 for men and 0.80 for women; CONCLUSION A modified diet history method combining a food record and a food frequency questionnaire shows good reproducibility.
Heteroresistance to Cephalosporins and Penicillins in Acinetobacter baumannii

ABSTRACT Heteroresistance to antimicrobial agents may affect susceptibility test results and therapeutic success. In this study, we investigated heteroresistance to cephalosporins and penicillins in Acinetobacter baumannii, a major pathogen causing nosocomial infections. Two A. baumannii isolates exhibited heteroresistance to ampicillin-sulbactam, ticarcillin-clavulanic acid, cefepime, and cefpirome, showing a distinct colony morphology of circular rings within the inhibition halos. Pulsed-field gel electrophoresis (PFGE) and outer membrane protein (OMP) analysis demonstrated that subpopulations around the disks/Etest strips and the original strains all belonged to the same PFGE type and OMP profile. Population analysis profile (PAP) showed the presence of heteroresistant subpopulations with high cefepime resistance levels in two isolates (008 and 328). Interestingly, A. baumannii 008 contained two peaks: one was grown in the presence of up to 1 μg of cefepime/ml, the other apparently occurred when the concentration of cefepime was raised to 256 μg/ml. After serial passages without exposure to cefepime, the PAP curve maintained the same trend observed for the original strain of A. baumannii 008. However, the PAP curve showed a shift to relatively lower cefepime resistance (from 256 to 64 μg/ml) in A. baumannii 328 after 10 passages in antibiotic-free Mueller-Hinton agar plates. Convergence to a monotypic resistance phenotype did not occur. Growth rate analysis revealed that slower growth in resistant subpopulations may provide a strategy against antibiotic challenge. To our knowledge, this is the first report of heteroresistance to cephalosporins and penicillins in A. baumannii.
Selegiline Ameliorates Depression-Like Behavior in Mice Lacking the CD157/BST1 Gene, a Risk Factor for Parkinson’s Disease

Parkinson’s disease (PD), a neurodegenerative disorder, is accompanied by various non-motor symptoms including depression and anxiety, which may precede the onset of motor symptoms. Selegiline is an irreversible monoamine oxidase-B (MAO-B) inhibitor, and is widely used in the treatment of PD and major depression. However, there are few reports about the effects of selegiline on non-motor symptoms in PD. The aim of this study was to explore the antidepressant and anxiolytic effects of selegiline, using CD157/BST1 knockout (CD157 KO) mouse, a PD-related genetic model displaying depression and anxiety, compared with other antiparkinsonian drugs and an antidepressant, and was to investigate the effects of selegiline on biochemical parameters in emotion-related brain regions. A single administration of selegiline (1–10 mg/kg) dose-dependently reduced immobility time in the forced swimming test (FST) in CD157 KO mice, but not C57BL/6N wild-type (WT) mice. At 10 mg/kg, but not 3 mg/kg, selegiline significantly increased climbing time in CD157 KO mice. A single administration of the antiparkinsonian drugs pramipexole (a dopamine (DA) D2/D3 receptor agonist) or rasagiline (another MAO-B inhibitor), and repeated injections of a noradrenergic and specific serotonergic antidepressant (NaSSA), mirtazapine, also decreased immobility time, but did not increase climbing time, in CD157 KO mice. The antidepressant-like effects of 10 mg/kg selegiline were comparable to those of 10 mg/kg rasagiline, and tended to be stronger than those of 1 mg/kg rasagiline. After the FST, CD157 KO mice showed decreases in striatal and hippocampal serotonin (5-HT) content, cortical norepinephrine (NE) content, and plasma corticosterone concentration. A single administration of selegiline at 10 mg/kg returned striatal 5-HT, cortical NE, and plasma corticosterone levels to those observed in WT mice. In the open field test (OFT), repeated administration of mirtazapine had anxiolytic effects, and selegiline nonsignificantly ameliorated anxiety-like behaviors in CD157 KO mice. In the social interaction and preference tests, repeated mirtazapine ameliorated the high anxiety and low sociability of CD157 KO mice, whereas selegiline did not. These results indicate that selegiline has antidepressant and mild anxiolytic effects in CD157 KO mice, and suggest that it is an effective antiparkinsonian drug for depressive and anxiety symptoms in PD patients with a CD157 single nucleotide polymorphism (SNP).
Near-Infrared Fluorescence with Indocyanine Green for Diagnostics in Urology: Initial Experience

Introduction Fluorescence imaging with indocyanine green is used in urology for the detection of sentinel lymph nodes and identification of prostate margins in radical prostatectomy for delineation of resection zone and selective clamping of vessels in partial nephrectomy; for identification and evaluation of length of ureteral strictures; for assessment of perfusion and viability of anastomoses during reconstructive stage of cystectomy. Safety of this technique is proven, while its diagnostic value and usefulness is still controversial. Methods This pilot study of using the SPY Elite Fluorescence Imaging System for diagnostics was performed in the I.M. Sechenov First Moscow State Medical University. Ten patients were enrolled: four patients underwent retropubic RP and lymph node dissection, five patients underwent partial nephrectomy, and one patient underwent ureteroplasty. Fluorophore was injected transrectally with TRUS guidance during RP in order to assess the lymph nodes. During partial nephrectomy, the compound was injected intravenously to differentiate the tumor from parenchyma by its blood supply. During ureteroplasty, the indocyanine green solution was injected into the renal pelvis to dye the ureter and locate the stricture. Results Sensitivity of this technique for visualization of sentinel lymph nodes was 100%, and specificity was 73.3%. In patients who underwent partial nephrectomy, all lesions were malignant and hypofluorescent when compared with healthy parenchyma. SPY allowed us to determine the location and extension of the stricture during ureteroplasty. No hypersensitivity reactions or complications were observed during injection of the compound.