Miracle-dz/UniFAR-FTUs huggingface dataset:
The E ect of Grid Resolution on the Accuracy of Tomographic Reconstruction Using a Plenoptic Camera

A novel 3-D, 3-C PIV technique is described, based on volume illumination and a plenoptic camera to measure a velocity eld. This technique is based on lighteld photography, which uses a dense microlens array mounted near a camera sensor to sample the spatial and angular distribution of light entering the camera. Tomographic algorithms (MART) are then used to reconstruct a volumetric intensity eld after the image is taken, and crosscorrelation algorithms extract the velocity eld from the reconstructed volume. This paper provides an introduction to the concepts of light elds and describes the tomographic algorithms used to reconstruct the measurement volume. A preliminary test on the accuracy of single particle reconstructions is presented, showing that spatially we can expect errors to be less than a voxel for most cases. Both a standard and double grid resolution volume are used in these simulations and conclusions are drawn between them. Finally a simulated Oseen vortex is presented showing a full simulation.
The role of experience in the assessment of pain in others

Person experiencing pain is usually the most competent one to indicate intensity and unpleasantness of the pain he/she is feeling. However, self-reports of pain are not always possible to obtain, so different methods must be used - one of them is assessment of pain experience conducted by another individual, a professional or an outsider. Since experience usually improves individual’s efficacy in a certain field, it would be expected that professionals - who assess pain on daily basis, would be more accurate in such task than outsiders - who have no experience with such assessment. The aim of this study was to investigate whether level of observer's experience with assessment of pain in others affects such assessment accuracy in experimentally induced pain. Observers, 32 students and 31 nurses, watched 6 video-tapes (3 volunteers in 2 different experimentally induced painful situations) and rated pain experience of the person on the tape. Results show no statistically significant difference between two samples ; both samples generally underestimated pain intensity and unpleasantness - indicating that everyday experience with assessment of pain in others does not improve efficacy in that task. Such finding suggests necessity of educational intervention which would enhance assessment accuracy of medical staff. Further studies are needed to investigate possible difference between professionals and outsiders in assessment accuracy of pain experienced in clinical conditions.
Active reduction of the two-way diffraction from a noise barrier by using feedforward control

This paper develops a feedforward (FF) structure based active noise control (ANC) system that reduces the two-way diffraction from an office partition with the aim of actively creating isolated acoustic domains in open-plan offices. The FF-ANC system can only reduce the noise downstream of the reference sensor due to the causality requirement. Therefore, a coupled FF control structure is proposed to realize the reduction of two-way diffraction. This system applies a two-source loudspeaker array as the control source, and two microphones as the reference and error sensors. The directivity of the loudspeaker array is controlled to emit the control sound only into the corresponding control area. In comparison with the preceding active diffraction reducing systems, using a directivity controlled loudspeaker array can generate an absorptive acoustic boundary rather than a reflective boundary on the diffracting edge, which can isolate the acoustic environment without adding reverberation in a room. The effectiveness of the proposed system is verified by computer simulations.
Association of Androgen Excess with Glucose Intolerance in Women with Polycystic Ovary Syndrome

Women with polycystic ovary syndrome (PCOS) show high prevalence of glucose intolerance. This study aimed to investigate the association of androgen excess with glucose intolerance in PCOS. A total of 378 women with PCOS participated in the study. Free androgen index (FAI) was selected as indicator of hyperandrogenism. Insulin sensitivity was assessed by 1/homeostasis model assessment of insulin resistance (1/HOMA-IR) and Matsuda insulin sensitivity index (ISIM); β-cell function was assessed by disposition index (DI). We found that women with glucose intolerance had higher FAI levels compared to women with normal glucose tolerance (NGT) (prediabetes 6.2, T2DM 7.9 versus NGT 5.0, resp.; p < 0.001). Furthermore, there was a direct association between FAI levels and frequency of glucose intolerance (OR = 2.480, 95% CI 1.387–4.434), even after adjusting for age, BMI, waist circumference, hypertension, fasting insulin, testosterone, SHBG, and family history of diabetes. In addition, with FAI increase, glycosylated hemoglobin (HbA1c), plasma glucose concentrations, and serum insulin levels increased, while insulin sensitivity and β-cell function decreased. Our results suggested that androgen excess indicated by high FAI levels might serve as indicator of glucose intolerance, as it might promote insulin resistance and β-cell dysfunction in women with PCOS.
Distance determination from dysprosium induced relaxation enhancement: a case study on membrane-inserted WALP23 polypeptides

Membrane incorporated synthetic α-helical polypeptides labelled with Dy(III) chelate complexes and nitroxide radicals were studied by the inversion recovery (IR) technique and Dy(III)-nitroxide distances were obtained. A comparison of obtained distances with the previously reported Gd(III)-nitroxide double electron–electron resonance (DEER) calibration data was performed and revealed reliability of the IR-based technique for the distance determination in membrane-incorporated biomacromolecules. The presented distance determination technique is ‘spectroscopically orthogonal’ to DEER-based distance measurements and can be potentially combined with DEER to study multiply spin-labelled biomacromolecules. The key steps of the data processing, the types of obtained distance information and the areas of possible application of the technique are discussed.
How Effective Are Incident-Reporting Systems for Improving Patient Safety? A Systematic Literature Review.

CONTEXT Incident-reporting systems (IRSs) are used to gather information about patient safety incidents. Despite the financial burden they imply, however,little is known about their effectiveness. This article systematically reviews the effectiveness of IRSs as a method of improving patient safety through organizational learning. METHODS Our systematic literature review identified 2 groups of studies: (1)those comparing the effectiveness of IRSs with other methods of error reporting and (2) those examining the effectiveness of IRSs on settings, structures, and outcomes in regard to improving patient safety. We used thematic analysis to compare the effectiveness of IRSs with other methods and to synthesize what was effective, where, and why. Then, to assess the evidence concerning the ability of IRSs to facilitate organizational learning, we analyzed studies using the concepts of single-loop and double-loop learning. FINDINGS In total, we identified 43 studies, 8 that compared IRSs with other methods and 35 that explored the effectiveness of IRSs on settings, structures,and outcomes. We did not find strong evidence that IRSs performed better than other methods. We did find some evidence of single-loop learning, that is, changes to clinical settings or processes as a consequence of learning from IRSs, but little evidence of either improvements in outcomes or changes in the latent managerial factors involved in error production. In addition, there was insubstantial evidence of IRSs enabling double-loop learning, that is, a cultural change or a change in mind-set. CONCLUSIONS The results indicate that IRSs could be more effective if the criteria for what counts as an incident were explicit, they were owned and ledby clinical teams rather than centralized hospital departments, and they were embedded within organizations as part of wider safety programs.
Additional Plots and Subsidiary analyses for Thomas, M. S. C., Knowland, V. C. P., & Karmiloff-Smith, A. (2011). Variability in the severity of developmental disorders: A neurocomputational account of developmental regression in autism

Developmental disorders show wide variations in severity even when, on genetic grounds, it is known that there is a common underlying cause. We used connectionist models of development combined with population modelling techniques to explore possible mechanistic causes of variations in disorder severity. Specifically, we investigated the plausibility of the hypothesis that disorder variability stems from the interaction of the common cause of the disorder with variations in neurocomputational parameters also present in the wider typically developing population. We base our simulations on a model of developmental regression in autism, which proposes that this phenomenon arises from over-aggressive synaptic pruning (Thomas, Knowland & Karmiloff-Smith, 2011). We simulated a population of 1000 networks in which 641 exhibited the behavioural marker of regression in their developmental trajectories when learning a notional cognitive domain. Aside from the known single cause of the disorder (an atypical connectivity pruning parameter), we then analysed which neurocomputational parameters contributed to variation observed in a number of characteristics of developmental regression. These included the timing of regression onset, its severity, its behavioural specificity, and the speed and extent of subsequent recovery. Results are related to existing causal frameworks to explain the origins of developmental deficits.
ASSOCIATION OF LIPOPROTEIN-α WITH OBESITY IN CHILDREN AND ADOLESCENTS IN DISTRICT SWAT

Background: Studies have demonstrated that atherosclerosis has its silent beginning during childhood. Coronary artery disease, particularly when it presents early in adult life has been observed to have a familial tendency. Lipoprotein-α [Lp-α], has a strong genetic association and raised levels when combined with obesity increase the risk of premature coronary heart disease. Thus in adults, has emerged the possibility of preventing or delaying the coronary artery disease when appropriate measures are applied early in life. In our study, we assessed the prevalence of overweight and obesity and its association with Lp-α in the child population of district Swat. Methods: The study was carried out in Saidu Teaching Hospital and Biochemistry Department, Saidu Medical College, Swat, from May to July 2007. Both boys and girls between 10–20 years of age were included. The prevalence of obesity was detected in 200 subjects by using body mass index. One hundred subjects were selected to compare the anthropometric and cardiovascular parameters of obese subjects with control group. Lp-α was measured in children of both the groups. Results: The prevalence of obesity in adolescent boys was 6.7% and that in adolescent girls was 10%. The prevalence was higher in female subjects, compared to male subjects. Obese subjects had significantly higher weight, body mass index, blood pressure values and Lp-α levels as compared to control group. Conclusion: Lipoprotein-α level is higher in obese children and adolescents than in non-obese. Keywords: Lipoprotein-α, Lp-α, Body mass index (BMI), Blood pressure (BP), Obesity
Association between T-182C, G1287A polymorphism in NET gene and suicidality in major depressive disorder in Chinese patients

Abstract Objective: Previous studies have implicated norepinephrine transporter gene (NET) polymorphisms in the etiology of major depressive disorder (MDD). A functional NET T-182C polymorphism (rs2242446) in the promoter region and a synonymous polymorphisms G1287A in the exon 9 (rs5569) were associated with MDD in different populations. However, few studies have focused on the relationship between these polymorphisms and MDD patients with suicidality. The objective of the present study was to examine whether the two polymorphisms are associated with MDD patients with suicidality in the Han Chinese population. Methods: Two hundred and sixty-three suicidal depressed patients and 241 non-suicidal depressed patients who met DSM-IV criteria for MDD were recruited from our hospital. Three hundred and three unrelated, age- and sex-matched healthy control subjects participated in this case-control study. Suicidality was assessed using Mini International Neuropsychiatric Interview (MINI) and the Hamilton rating scale for depression (HAMD). Genotypes of T-182C polymorphism (rs2242446) and G1287A (rs5569) were screened by polymerase chain reaction. Results: No statistical significant differences between patients and controls were found for any of the analysed polymorphisms, either in the genotype or allele distribution. Conclusions: Our results suggest that the investigated polymorphisms are not major susceptibility factors in the etiology of MDD with suicidality. However, the results must be verified in larger samples and different ethnicities.
Synthesis, activity, and docking studies of eugenol‐based glucosides as new agents against Candida sp.

Seventeen new synthetic derivatives of eugenol (6, 8–15 and 8′‐15′) were planned following literature reports on antifungal activities of nitroeugenol and eugenol glucoside. The anti‐Candida activity of these compounds was investigated by in vitro assay, and the cytotoxicity evaluation was performed with the most active compounds. The peracetylated glucosides presented better biological results than their hydroxylated analogues. The glucoside 11, a 4‐nitrobenzamide, showed the best potency (MIC50 range 11.0–151.84 μm), the wider spectrum of action, and overall the best selectivity indexes, especially against C. tropicalis (~30) and C. krusei (~15). To investigate its possible mechanism of action, glucoside 11 was subjected to molecular docking studies with Candida sp. enzymes involved in ergosterol biosynthesis. Results have shown that the peracetyl glucosyl moiety and the 4‐nitrobenzamide group in 11 are effectively involved in its high affinity with the active site of squalene epoxidase.
Cognitive decline in late-life: biological markers and early identification of persons at risk for dementia

In this prospective study we examined whether total cholesterol and the oxysterols 24Sand 27-hydroxycholesterol were related to cognitive performance and rate of cognitive decline in elderly, and whether these associations were modified by ApoE e4. Data were collected during six years of follow-up as part of the Longitudinal Aging Study Amsterdam (N = 1,181, age > 65 years), and analyzed using generalized estimating equations. Cognitive performance was measured with the Mini-Mental State Examination (general cognition), the Auditory Verbal Learning Test (memory) and the Coding Task (information processing speed). Lower cholesterol at baseline was negatively associated with both general cognition (p = 0.012) and information processing speed (p = 0.045). ApoE modified the association between cholesterol and cognitive decline, and the association between the ratio of 27-hydroxycholesterol to cholesterol and cognitive functioning. In ApoE e4 carriers, lower cholesterol was related to a higher rate of decline on information processing speed (p = 0.006), and a higher ratio of 27-hydroxycholesterol to cholesterol was related to a lower level of general performance (p = 0.002) and memory functioning (p = 0.045). The results implicate that lower total cholesterol may be considered as a frailty marker, predictive of lower cognitive functioning in elderly.
The characteristics of invasive fishes : what has been learned so far ?

Invasive species are increasingly recognized as one of the main threats to biodiversity and both an urgent need and a unique tool for ecological research. Although attempts to identify future invasive species are not new to ecology, rigorous quantitative analyses emanate mostly from the last decade. In 2001, quantitative studies dealing with the distinguishing ecological features of invasive species were reviewed but no papers on fish species were identified. Subsequently, several quantitative studies have addressed this issue for freshwater fishes, including those that have focused on California, Colorado, the Great Lakes of North America and the Iberian Peninsula. In the present paper, 12 such studies are reviewed and compared with regard to their conclusions and methodology. The issues of different invasion stages and comparison strategies, propagule pressure, information-theoretic analyses v. sequential techniques, use of phylogenetic comparative methods and spatial scale are discussed. Non-native fish transport and release are the least investigated although taxonomy and human interests seem key in these first initial stages. Establishment success, which has received more study, seems more multi-factorial, context-dependent and more mediated by species-specific life-history traits. The dispersal and impact phases are less understood, although the comparison of traits (and taxonomy) between native and invasive species and particularly its variability holds promise. The lack of data on propagule pressure and the use of sequential techniques for observational data sets with many intercorrelated variables could affect the conclusions of previous studies. Research on the dispersal, impact and particularly transport and introduction phases should be prioritized rather than establishment. All the studies identified were at temperate latitudes in the northern hemisphere; studies in other regions and comparison of different regions and multiple scales are lacking. # 2007 The Author
Greenhouse gas emissions and reactive nitrogen releases from rice productionwith simultaneous incorporation of wheat straw and nitrogen fertilizer

Abstract. Impacts of simultaneous inputs of crop straw and nitrogen (N) fertilizer on greenhouse gas (GHG) emissions and N losses from rice production are not well understood. A 2-year field experiment was established in a rice–wheat cropping system in the Taihu Lake region (TLR) of China to evaluate the GHG intensity (GHGI) as well as reactive N intensity (NrI) of rice production with inputs of wheat straw and N fertilizer. The field experiment included five treatments of different N fertilization rates for rice production: 0 (RN0), 120 (RN120), 180 (RN180), 240 (RN240), and 300 kg N ha−1 (RN300, traditional N application rate in the TLR). Wheat straws were fully incorporated into soil before rice transplantation. The meta-analytic technique was employed to evaluate various Nr losses. Results showed that the response of rice yield to N rate successfully fitted a quadratic model, while N fertilization promoted Nr discharges exponentially (nitrous oxide emission, N leaching, and runoff) or linearly (ammonia volatilization). The GHGI of rice production ranged from 1.20 (RN240) to 1.61 kg CO2 equivalent (CO2 eq) kg−1 (RN0), while NrI varied from 2.14 (RN0) to 10.92 g N kg−1 (RN300). Methane (CH4) emission dominated the GHGI with a proportion of 70.2–88.6 % due to direct straw incorporation, while ammonia (NH3) volatilization dominated the NrI with proportion of 53.5–57.4 %. Damage costs to environment incurred by GHG and Nr releases from current rice production (RN300) accounted for 8.8 and 4.9 % of farmers' incomes, respectively. Cutting N application rate from 300 (traditional N rate) to 240 kg N ha−1 could improve rice yield and nitrogen use efficiency by 2.14 and 10.30 %, respectively, while simultaneously reducing GHGI by 13 %, NrI by 23 %, and total environmental costs by 16 %. Moreover, the reduction of 60 kg N ha−1 improved farmers' income by CNY 639 ha−1, which would provide them with an incentive to change the current N application rate. Our study suggests that GHG and Nr releases, especially for CH4 emission and NH3 volatilization, from rice production in the TLR could be further reduced, considering the current incorporation pattern of wheat straw and N fertilizer.
Transient pausing by RNA polymerase II

RNA polymerase II (Pol II) elongation control is utilized during transcription of most metazoan genes (1). Polymerases that successfully initiate must first break contacts with initiation factors and then interact with elongation factors including the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF). This leads to a reduction of the elongation rate due to an increase in pausing. The stage is now set for positive transcription elongation factor b (P-TEFb) to phosphorylate DSIF, which, in turn, leads to the loss of NELF, association of the PAF1 complex, and the onset of productive elongation. Although it is clear that paused Pol II is found in promoter-proximal regions of most expressed genes in metazoan cells, a controversy has arisen concerning how long paused polymerases remain engaged. The prevailing view is that paused Pol II is relatively stable. However, the findings presented in PNAS by Steurer et al. (2) call this view into question. They generated a human cell line solely expressing GFP-tagged Pol II and then used fluorescence recovery after photobleaching (FRAP) to identify and characterize four distinguishable kinetic states for Pol II. Besides the very rapid recovery due to diffusion of free Pol II, they found three bound states, each with about an order of magnitude slower recovery than the preceding one. These kinetic states were assigned to initiation, pausing, and productive elongation by observing how well-characterized compounds affected the FRAP measurements. Steurer et al. (2) used computational modeling of the FRAP data to calculate the residence time for Pol II in each of the three bound states, as well as the fraction of each state that progresses into the next state (Fig. 1). They found that in normal untreated cells, Pol II spends, on average, 2.4 s interacting with the promoter. About 90% of these polymerases dissociate because … [↵][1]1Email: david-price{at}uiowa.edu. [1]: #xref-corresp-1-1
Qualitative and Quantitative Detection of Botulinum Neurotoxins from Complex Matrices: Results of the First International Proficiency Test

In the framework of the EU project EQuATox, a first international proficiency test (PT) on the detection and quantification of botulinum neurotoxins (BoNT) was conducted. Sample materials included BoNT serotypes A, B and E spiked into buffer, milk, meat extract and serum. Different methods were applied by the participants combining different principles of detection, identification and quantification. Based on qualitative assays, 95% of all results reported were correct. Successful strategies for BoNT detection were based on a combination of complementary immunological, MS-based and functional methods or on suitable functional in vivo/in vitro approaches (mouse bioassay, hemidiaphragm assay and Endopep-MS assay). Quantification of BoNT/A, BoNT/B and BoNT/E was performed by 48% of participating laboratories. It turned out that precise quantification of BoNT was difficult, resulting in a substantial scatter of quantitative data. This was especially true for results obtained by the mouse bioassay which is currently considered as “gold standard” for BoNT detection. The results clearly demonstrate the urgent need for certified BoNT reference materials and the development of methods replacing animal testing. In this context, the BoNT PT provided the valuable information that both the Endopep-MS assay and the hemidiaphragm assay delivered quantitative results superior to the mouse bioassay.