Miracle-dz/UniFAR-FTUs huggingface dataset:
Using multiple perspectives to interpret empirical results: Does it add value to the interpretation?

Can value be added to the interpretation of research results if different perspectives to view research results are used? It is the contention of the authors that it is possible to get a richer interpretation of research findings by reviewing the results more than once, using more than one interpretive perspective. After a first round of interpretation was done, using Habermas' knowledge interests, hermeneutics and Giddens' 'consequences of contemporary modernity' as perspectives, certain concepts in the abundance of empirical results emerged as being more important than others. A further round of interpretation (using Klein and Myers' principles for evaluating interpretive studies) was done to refine the model in order to derive a conceptual framework.
Sensitive and selective detection of mycoplasma in cell culture samples using cantilever sensors

In this article we report a new biosensor‐based method that is more sensitive and rapid than the current approach for detecting mycoplasma in cell culture samples. Piezoelectric‐excited millimeter‐sized cantilever (PEMC) sensors respond to mass change via resonant frequency change. They are sensitive at femtogram level and can be used directly in liquid for label‐free detection. Common cell culture contaminant, Acholeplasma laidlawii was detected in both buffer and cell culture medium. Two different sources (positive control from a commercial kit and ATCC 23206) were analyzed using antibody‐immobilized PEMC sensor. Resonant frequency decrease caused by binding of A. laidlawii was monitored in real‐time using an impedance analyzer. Positive detection was confirmed by a second antibody binding. The limit of detection (LOD) was lower than 103 CFU/mL in cell culture medium using PEMC sensor while parallel ELISA assays showed LOD as 107 CFU/mL. This study shows that PEMC sensor can be used for sensitive and rapid mycoplasma detection in cell culture samples. Biotechnol. Bioeng. 2010;105: 1069–1077. © 2009 Wiley Periodicals, Inc.
Follow‐up to paper by S. Wolter, M. Schüttpelz, M. Tscherepanow, S. van de Linde, M. Heilemann and M. Sauer, entitled Real‐Time Computation of Subdiffraction‐Resolution Fluorescence Images

We are proud to announce that the rapid, accurate program implementing direct stochastic optical reconstruction microscopy (rapidSTORM) algorithm and implementation presented in the article entitled ‘Real-Time Computation of Subdiffraction-Resolution Fluorescence Images’ by Wolter et al. (2010) has recently been published as free and open source software and is, to our knowledge, the most extensive and feature-rich open source program for single molecule localization microscopy evaluation. The rapidSTORM software package aids super-resolution fluorescence microscopy by localizing single fluorescent molecules in image stacks produced by methods such as photoactivated localization microscopy (PALM), fluorescence photoactivation localization microscopy (FPALM), stochastic optical reconstruction microscopy (STORM), direct stochastic optical reconstruction microscopy (dSTORM) or ground state depletion microscopy followed by individual molecule return (GSDIM) (van de Linde et al., 2011). This localization is performed by finding likely fluorescent molecule positions (spots) in an image stack via maximum finding in a noisereduced image, wherefore a number of approaches such as average mask smoothing, Gaussian smoothing and the morphological fillhole operation are available. Fluorophore positions are nanometer-precisely localized via full nonlinear least-squares optimization. These localizations can be stored, filtered and postprocessed in a number of ways, including advanced auto-contrast imaging. rapidSTORM is capable of processing input data in real time, i.e. faster than the acquisition, with full Gaussian least-squares fitting, and thus supports imaging in less than ∼20 s when combined with the dSTORM method (Wolter et al., 2010). Many current developments in super-resolution fluorescence imaging are supported by rapidSTORM. Dense emitter
Characterization of Vibrio vulnificus isolated from retail cockle and shrimp by plasmid profiling and antibiotic susceptibility test (Pencirian Vibrio vulnificus yang dipencilkan daripada kerang dan udang dengan profil plasmid dan ujian kerentanan antibiotik)

Of the 148 cockle (Anadara granosa) and 433 shrimp (Paneus indicus) samples examined, 27% and 6.9% were positive for Vibrio vulnificus, respectively. Twenty-nine and 21 isolates from cockles and shrimps were examined for their antibiotic resistance. All isolates showed resistance to one or more of the antibiotics tested. In transconjugation tests, no relationship was found between the high molecular weight plasmid (35.8 MDa) detected in several isolates and their resistance phenotypes, indicating that their antibiotic resistance is chromosomal. Plasmid profiles and antibiotic resistance patterns were used as a preliminary approach to type, at strain level, the isolates from cockles and shrimps. Analysis by antibiotic resistance patterns showed a high phenotypic polymorphism. However, the high number of isolates devoid of plasmid rendered this technique less useful. These results indicate that multiresistant V. vulnificus
Enhancing Speech by Reconstruction from Robust Acoustic Features

A method of speech enhancement is developed that reconstructs clean speech from a set of acoustic features using a sinusoidal model of speech. This is a significant departure from traditional filtering-based methods of speech enhancement. A major challenge with this approach is to estimate accurately the acoustic features (voicing, fundamental frequency, spectral envelope) from noisy speech. This is achieved using maximum a-posteriori estimation methods that operate on the noisy speech. Objective results are presented to optimise the proposed system and a set of subjective tests compare the approach with traditional enhancement methods.
Interplay Between In-Plane and Out-of-Plane Resonances of Heptamer Oligomer Nanoapertures

In this study, the interaction of in-plane and out-of-plane resonances of heptamer oligomer nanoapertures is studied. Nanoaperture systems in this paper are investigated using the finite-difference time-domain method. Our results suggest that new plasmonic modes are created as a result of the in-plane plasmonic superradiant/ subradiant modes and out-of-plane modes due to the interaction of central and lateral nanoholes.
IMPACT OF KM PRACTICES ON FIRMS' PERFORMANCE: A MEDIATING ROLE OF BUSINESS PROCESS CAPABILITY AND ORGANIZATIONAL LEARNING

This study tends to examine the mediating role of business process capabilities and organizational learning in order to validate the KM practices driven performance. A mediating model is proposed and confirmatory factor analysis is performed through structural equation modeling to assess the overall measurement model. The results of the study confirm that KM practices have positive and significant association on overall performance of firms and as well intermediate measures (business process capability and organizational learning) have positive and significant connection with KM practices and overall performance of firms. Further, the results of the study reveal that KM practices are partially rooted through business process capabilities and completely mediated by organizational learning. It suggests that both intermediate measures are complementary for KM practices driven performance more specifically the organizational learning. The results of the study postulate that KM practices provide foundation to KM-driven performance, where business process capability and organization learning are two important drivers for value creation process. An organization has bundle of knowledge resources and capabilities, so it should dedicate its efforts to identify and implement more KM practices as well for the improvement of business process capabilities and organizational learning to better realized KM-oriented performance.
Optimally Predictive Causal Inference

Natural systems compute intrinsically and produce information. The organization of a stochastic dynamical system is reflected in the time series of observations made of the system and can be quantified by the excess entropy or predictive information—the mutual information between past and future. This information can be used to build models of varying complexity that capture the causal structure of the underlying system. Here we study two distinct cases of causal inference, which we call optimal causal filtering and optimal causal estimation. Optimal causal filtering corresponds to the ideal case in which infinite data are available. We show that, in the limit in which a model complexity constraint is relaxed, the filtering method finds the causal architecture of a stochastic dynamical system, known as the causal state partition. In that limit, it reconstructs exactly the system’s hidden, causal states. More generally, it finds a graded model-complexity hierarchy of approximations to the causal architecture. For nonideal cases with finite data, we show how the correct number of underlying causal states can be found by optimal causal estimation. A previously derived model complexity control term allows us to correct for the effect of statistical fluctuations in probability estimates and thereby avoid over-fitting.
Proposal of classification method of bus operation states using sensor data

In bus companies, it is important for the operation manager to grasp operation states of the vehicle from the viewpoint of safety management and improving the operation efficiency. Currently, for allowing the operation manager to grasp operation states of the vehicle, the driver records operation states by manually operating a recorder called ‘Digital-tachograph’. However, operating a digital tachograph is a heavy burden to the driver. In this research, in order to solve this problem and to realize efficient operation, we propose a method for automatic classification of operation states using sensor data obtained from the buses. We implemented a classifier using Random Forest with the sensor data. The correct answer rate was 0.9 or more in each condition unless it was irregular operation.
The analysis of respiratory sinus arrhythmia using spectral analysis and digital filtering.

Respiratory sinus arrhythmia is the phenomenon by which respiration modulates heart rate in normal humans and in many animals. This investigation was divided into the following three categories: 1) the development of a mathematical model relating respiration to those variations that it causes in heart rate; 2) the use of digital filtering techniques to attenuate fluctuations in heart rate which are due to respiration; and 3) the development of methods that use only heart rate to get information about respiration.
Health-related quality of life and financial impact of caring for a child with Thalassaemia Major in the UK.

BACKGROUND Thalassaemia Major (TM) is a serious condition characterized by life-long dependence on blood transfusions and chelation therapy. Our aim was to determine health-related quality of life (HRQOL) in children with TM living in the UK, and the impact of caring for a child receiving National Health Service treatment on family finances. METHODS This was a cross-sectional assessment of HRQOL in children (n= 22) with TM aged 8-18 years. Children were recruited from three UK Paediatric Haematology and Bone Marrow Transplant centres. Mothers completed measures of their child's HRQOL [PedsQL 4.0 (Measurement Model for the Pediatric Quality of Life Inventory, James W. Varni PhD, PedMetrics, Quantifying the Qualitative SM, Copyright 1998-2009)] and behaviour (Strengths and Difficulties questionnaire), and the impact of caring for the child on family finances. RESULTS Child behaviour was within the normal range but child HRQOL was significantly lower than population norms. Family financial concerns associated with TM were associated with poorer child HRQOL (P= 0.020). CONCLUSIONS Thalassaemia Major poses a considerable challenge to child HRQOL, well documented in areas of the world where TM is prevalent. Despite the availability of National Health Service care and financial benefits our study suggests a similar burden in the UK.
IFN‐γ receptor deficiency prevents diabetes induction by diabetogenic CD4+, but not CD8+, T cells

IFN‐γ is generally believed to be important in the autoimmune pathogenesis of type 1 diabetes (T1D). However, the development of spontaneous β‐cell autoimmunity is unaffected in NOD mice lacking expression of IFN‐γ or the IFN‐γ receptor (IFNγR), bringing into question the role IFN‐γ has in T1D. In the current study, an adoptive transfer model was employed to define the contribution of IFN‐γ in CD4+ versus CD8+ T cell‐mediated β‐cell autoimmunity. NOD.scid mice lacking expression of the IFNγR β chain (NOD.scid.IFNγRBnull) developed diabetes following transfer of β cell‐specific CD8+ T cells alone. In contrast, β cell‐specific CD4+ T cells alone failed to induce diabetes despite significant infiltration of the islets in NOD.scid. IFNγRBnull recipients. The lack of pathogenicity of CD4+ T‐cell effectors was due to the resistance of IFNγR‐deficient β cells to inflammatory cytokine‐induced cell death. On the other hand, CD4+ T cells indirectly promoted β‐cell destruction by providing help to CD8+ T cells in NOD.scid. IFNγRBnull recipients. These results demonstrate that IFN‐γR may play a key role in CD4+ T cell‐mediated β‐cell destruction.
Deep brain stimulation of the subthalamic nucleus improves intrinsic alertness in Parkinson's disease

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is a treatment option for patients with Parkinson's disease (PD) in the advanced stage. Besides motor improvement, DBS of the STN may also modulate cognitive and attentional functions of the basal ganglia. In our study, 13 patients with PD and bilateral DBS of the STN were assessed with DBS switched on and off by the use of a wide range of neuropsychological tasks. This included reasoning, cognitive flexibility, phonemic and semantic word fluency, verbal and nonverbal short‐term memory, learning, delayed verbal memory recall, and stimulus‐response incompatibility. Special emphasis was put on basic attentional functions, in particular intrinsic and phasic alertness as well as visual search. DBS significantly improved intrinsic alertness, whereas phasic alertness and other neuropsychological domains were not affected. Additionally, the effects on intrinsic alertness were independent of motor improvements by DBS. The findings suggest that DBS modulates the fronto‐parietal network of alertness. © 2009 Movement Disorder Society
Polarized light imaging of white matter architecture

Polarized light imaging (PLI) is a method to image fiber orientation in gross histological brain sections based on the birefringent properties of the myelin sheaths. The method uses the transmission of polarized light to quantitatively estimate the fiber orientation and inclination angles at every point of the imaged section. Multiple sections can be assembled into a 3D volume, from which the 3D extent of fiber tracts can be extracted. This article describes the physical principles of PLI and describes two major applications of the method: the imaging of white matter orientation of the rat brain and the generation of fiber orientation maps of the human brain in white and gray matter. The strengths and weaknesses of the method are set out. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
Supplementation with a blend of krill and salmon oil is associated with increased metabolic risk in overweight men.

BACKGROUND Krill is an increasingly popular source of marine n-3 (ω-3) PUFA that is seen as a premium product. However, to our knowledge, the effect of krill-oil supplementation on insulin sensitivity in humans has not been reported. OBJECTIVE We assessed whether supplementation with a blend of krill and salmon (KS) oil [which is rich in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)] affects insulin sensitivity in overweight men. DESIGN The design was a randomized, double-blind, controlled crossover trial. A total of 47 men with a mean ± SD age of 46.5 ± 5.1 y, who were overweight [body mass index (in kg/m(2)) from 25 to 30] but otherwise healthy, received 5 1-g capsules of KS oil or a control (canola oil) for 8 wk and crossed over to another treatment after an 8-wk washout period. The primary outcome was insulin sensitivity assessed by using the Matsuda method from an oral-glucose-tolerance test. Secondary outcomes included lipid profiles, inflammatory markers, 24-h ambulatory blood pressure, and carotid artery intimamedia thickness. RESULTS Unexpectedly, insulin sensitivity (per the Matsuda index) was 14% lower with the KS oil than with the control oil (P = 0.049). A mediation analysis showed that, after controlling for the likely positive effects of blood EPA and DHA (i.e., the omega-3 index), the reduction in insulin sensitivity after KS-oil supplementation was more marked [27% lower than with the control oil (P = 0.009)]. CONCLUSIONS Supplementation with a blend of KS oil is associated with decreased insulin sensitivity. Thus, krill-oil supplementation in overweight adults could exacerbate risk of diabetes and cardiovascular disease. This trial was prospectively registered at the Australian New Zealand Clinical Trials Registry as ACTRN12611000602921.
Insights into the function of the phasiRNA-triggering miR1514 in response to stress in legumes

ABSTRACT We recently described the activity of miR1514a in response to water deficit in Phaseolus vulgaris. Pvu-miR1514a targets a NAC transcription factor mRNA for cleavage and subsequently triggers NAC-derived phasiRNA formation. Here we show that accumulation and activity of miR1514a are also conserved in the model legume Medicago truncatula. Consistently, we identified Mtr-miR1514a and detected its increased accumulation in response to stress conditions, targeting a NAC TF mRNA for cleavage and triggering phasiRNA production. In P. vulgaris, miR1514a inhibition in transgenic hairy roots was reported to increase NAC 700 mRNA levels and to affect expression patterns of several genes, including that of a Sec 14 homolog. We report here that in adult plant roots exposed to dehydration conditions, where miR1514a levels increased and NAC 700 mRNA decreased, there was a reduction of Sec 14 homolog mRNA levels, suggesting a direct transcriptional effect. The functions of miR1514a, NAC 700 and derived phasiRNAs have just begun to be elucidated in common bean; future understanding of their activities in this and other legumes species will advance our knowledge of microRNA functions in plants.
RIZ1 and histone methylation status in pituitary adenomas

RIZ1 displays strong tumor-suppressive activities, which has a potential histone methyltransferase activity. The objective of the study was to evaluate the level and the methylation status of RIZ1 and analyze its association with clinicopathological features and the histone in the pituitary adenomas. We found that RIZ1-positive cases were 11/50 and H-Scores 22.75 ± 11.83 in invasive pituitary adenomas and 26/53 and 66.3 ± 21.7 in non-invasive pituitary adenomas (χ2 = 8.182, p = 0.004). RIZ1 and C-myc showed the opposite trend in these cases. The methylation levels of RIZ1 were more than 50% in 30.4% (7/23) CpG sites through MALDI-TOF Mass array. There was significant difference (p < 0.01) in 4 CpG sites between invasive pituitary adenoma group and non-invasive pituitary adenoma group; furthermore, the relieved methylation levels of H3K4/H3K9 and enhanced methylation levels of H3K27 in the patients’ serum were found. Furthermore, there was statistic difference of H3K4 and H3K27 methylation between invasive pituitary adenoma and non-invasive pituitary adenoma group (p < 0.01). The average progression-free survival in high RIZ1 group was 52.63 ± 7.62 months and 26.06 ± 4.23 months in low RIZ1 group (p < 0.05). Promoter region methylation of RIZ1 may play an important role in the epigenetic silencing of RIZ1 expression in pituitary adenomas, which may translate into important diagnostic and therapeutic applications.
Original research article Falling through the cracks: contraceptive needs of female sex workers in Cambodia and Laos ☆,☆☆

Background: Condom is the only method promoted for dual protection among female sex workers (FSWs) in most Asian countries, which may be insufficient to prevent pregnancies given FSWs' high frequency of sexual intercourse. Study Design: Data were obtained from independent cross-sectional surveillance surveys conducted in Cambodia and Laos. Random samples of FSWs provided behavioral information. Results: Respondents numbered 592 in Cambodia and 1421 in Laos. In Cambodia, 28.2% had abortions in the past year despite reporting 99.0% condom use at last commercial sex. Abortion increased with the number of clients, inconsistent condom use, recent condom breakage and recent forced unprotected sex with clients. In Laos, 26.0% of all FSWs had ever aborted as had 89.4% of those who had been pregnant in the past 6 months. Conclusions: FSWs experience higher frequency of abortion than women from the general population. FSWs' reportedly high rate of condom use is insufficient to prevent pregnancies.
Adaptive radiation‐induced epigenetic alterations mitigated by antioxidants

Humans are exposed to low‐dose ionizing radiation (LDIR) from a number of environmental and medical sources. In addition to inducing genetic mutations, there is concern that LDIR may also alter the epigenome. Such heritable effects early in life can either be positively adaptive or result in the enhanced formation of diseases, including cancer, diabetes, and obesity. Herein, we show that LDIR significantly increased DNA methylation at the viable yellow agouti (Avy) locus in a sex‐specific manner (P=0.004). Average DNA methylation was significantly increased in male offspring exposed to doses between 0.7 and 7.6 cGy, with maximum effects at 1.4 and 3.0 cGy (P<0.01). Offspring coat color was concomitantly shifted toward pseudoagouti (P<0.01). Maternal dietary antioxidant supplementation mitigated both the DNA methylation changes and coat color shift in the irradiated offspring. Thus, LDIR exposure during gestation elicits epigenetic alterations that lead to positive adaptive phenotypic changes that are negated with antioxidants, indicating they are mediated in part by oxidative stress. These findings provide evidence that in the isogenic Avy mouse model, epigenetic alterations resulting from LDIR play a role in radiation hormesis, bringing into question the assumption that every dose of radiation is harmful. —Bernal, A. J., Dolinoy, D. C. , Huang, D. , Skaar, D. A. , Weinhouse, C. , Jirtle, R. J. Adaptive radiation‐induced epigenetic alterations mitigated by antioxidants. FASEB J. 27, 665–671 (2013). www.fasebj. org
InfarctSizer: computing infarct volume from brain images of a stroke animal model

Many computational methods for determining the infarct volume from the image of 2,3,5-triphenyltetrazolium chloride-stained brain slices rely on the discretion of the user to determine the infarct region by visual inspection. Once the user determines the infarct boundary by visual inspection, the methods compute the area within the boundary with the assumption that all the spots within the boundary have been infarcted at the same level. However, in the same brain image, partially infarcted spots often tend to appear pinkish whereas fully or severely infarcted spots appear white. We developed a program called InfarctSizer, which automatically detects the infarct region and computes the infarct volume proportional to infarction levels. Comparison of InfarctSizer with other methods shows that InfarctSizer computes the infarct volume more accurately and efficiently than other methods. InfarctSizer and sample brain images are available at http://wilab.inha. ac.kr/brainimage.