Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence, characterisation and antimicrobial resistance of Campylobacter and Salmonella in raw poultrymeat in the UK, 2003–2005

This study was conducted to determine the prevalence and antimicrobial resistance of Campylobacter and Salmonella isolates from retail poultrymeat in the UK during 2003–2005. Poultrymeat (n = 2104) were more frequently contaminated with Campylobacter (57.3%) than with Salmonella (6.6%). Chicken exhibited the highest contamination from Campylobacter (60.9%), followed by duck (50.7%), turkey (33.7%) and other poultrymeat (34.2%). Duck had the highest contamination from Salmonella (29.9%), compared with chicken (5.6%), turkey (5.6%), and other poultrymeat (8.6%). C. jejuni predominated in raw chicken, whereas C. coli predominated in turkey and duck. C. coli isolates were more likely to exhibit antimicrobial drug resistance, including quinolones, than C. jejuni. Salmonella Enteritidis was the most frequent Salmonella serotype isolated. Salmonella isolates from turkey exhibited higher rates of multiple drug resistance (55.6%) than isolates from chicken (20.9%) and duck (13.6%). The findings reinforce the importance of thorough cooking of poultrymeat and good hygiene to avoid cross-contamination.
Toward Realistic Modeling of a Shelfbreak Front: Lagrangian Metrics and Process Studies for the Middle Atlantic Bight

Abstract : A region where predictive capability is sought for tactical concerns is the flow field in the vicinity of the continental shelfbreak. Sound propagation from the continental slope to the continental shelf is a complex process that is highly dependent upon the oceanographic environment. A strong thermal shelfbreak front, and its associated current, are the key features that influence acoustic propagation in many shelf regions. Theory and field data suggest that acoustic propagation is strongly affected by frontal features that can evolve on rapid temporal scales (1-2 days) and small spatial scales (10-20 km). The overall aim of this proposed work is to improve our ability to realistically model and predict the evolution of the shelfbreak front so as to advance the predictive capability of this region.
Position control of hybrid pneumatic-electric actuators

The design, modeling and control of a novel hybrid pneumatic-electric actuator for applications in robotics and automation is presented. The design incorporates a pneumatic cylinder and DC motor connected in parallel. By avoiding the need for a high ratio transmission, the design greatly reduces the joint friction torque that contributes to the danger associated with robot arms. A novel discrete-valued model-predictive control (DVMPC) algorithm is proposed for controlling the position of the pneumatic cylinder with on/off valves, rather than costly proportional or servo valves. A variant of inverse dynamics control is proposed for the DC motor. A prototype was built for validating the actuator design and control algorithms. It is used to rotate a single-link robot arm. Experimental results are presented for vertical cycloidal and sinusoidal position trajectories. Even with the poor quantization caused by the on/off valves, the pneumatic cylinder controlled by the proposed DVMPC algorithm achieved a 2.5% maximum absolute error (MAE) for the vertical cycloidal trajectory. The DVMPC algorithm also switches the valves less often than the PWM method, reducing valve wear. With the addition of the DC motor to form the hybrid actuator, the performance improvement was significant. For the vertical cycloidal trajectory, the MAE was reduced to 0.37%. With the vertical sinusoidal trajectory, the MAE was 1.1%. These results compare favorably to the 5% MAE achieved by previous researchers for a horizontal sinusoidal trajectory using a hybrid pneumatic-electric actuator controlled by servo valves.
Alternative Methods Of Estimating Output Gap For Turkey

Output gap is defined as the difference between the potential output and actual output. There are several approaches used in the literature to estimate output gap. With this study it is aimed to obtain alternative output gap estimations for Turkish Economy, considering the constraints of approaches that are used in the literature. With this aim, output gap is estimated using two methods such as (1) Structural VAR (Sutructural Vector Autoregressive Model-SVAR) approach proposed in Blanchard and Quah (1989), and (2) Modified Hodrick Prescott Filter based on ARIMA model proposed in Kaiser ve Maravall (2005). These methods are compared to the most frequently used HP filter method in the literature. The output gap estimations are compared in terms of their actual inflation prediction power considering that output gap estimation is an essential input in structuring price stability policy. As a result it can be asserted that output gap estimated by SVAR method produces more successful results in predicting actual inflation.
Three Adenovirus E3 Proteins Cooperate to Evade Apoptosis by Tumor Necrosis Factor-related Apoptosis-inducing Ligand Receptor-1 and -2*

Adenovirus encodes multiple gene products that regulate proapoptotic cellular responses to viral infection mediated by both the innate and adaptive immune systems. The E3-10.4K and 14.5K gene products are known to modulate the death receptor Fas. In this study, we demonstrate that an additional viral E3 protein, 6.7K, functions in the specific modulation of the two death receptors for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). The 6.7K protein is expressed on the cell surface and forms a complex with the 10.4K and 14.5K proteins, and this complex is sufficient to induce down-modulation of TRAIL receptor-1 and -2 from the cell surface and reverse the sensitivity of infected cells to TRAIL-mediated apoptosis. Down-modulation of TRAIL-R2 by the E3 complex is dependent on the cytoplasmic tail of the receptor, but the death domain alone is not sufficient. These results identify a mechanism for viral modulation of TRAIL receptor-mediated apoptosis and suggest the E3 protein complex has evolved to regulate the signaling of selected cytokine receptors.
A Simple Confocal Microscopy-based Method for Assessing Sperm Movement

ABSTRACT In the field of reproductive medicine, assessment of sperm motility is a key factor for achieving successful artificial insemination, in vitro fertilization, or intracellular sperm injection. In this study, the motility of boar sperms was estimated using real-time imaging via confocal microscopy. To confirm this confocal imaging method, flagellar beats and whiplash-like movement angles were compared between fresh and low-temperature-preserved (17℃ for 24 h) porcine sperms. Low-temperature preservation reduced the number of flagellar beats from 11.0±2.3 beats/s (fresh sperm) to 5.7±1.8 beats/s and increased the flagellar bending angle from 19.8°±13.8° (fresh) to 30.6°±15.6°. These data suggest that sperm activity can be assessed using confocal microscopy. The observed motility patterns could be used to develop a sperm evaluation index and automated confocal microscopic sperm motility analysis techniques.
Adaptive DF Relaying Transmission for Security

This paper comprehensively studies the secure decode-and-forward (DF) relaying transmission in slow fading channels. To maximize the secrecy throughput under a secrecy outage probability constraint, we propose three adaptive transmission schemes (ATSs) with different complexity and flexibility, and design system parameters according to the instantaneous channel state information of the legitimate receiver. Specifically, in ATS-SW, source and relay use the same codeword, and eavesdropper employs the maximal ratio combining (MRC) reception; whereas in ATS-DWSR and ATS-DBDR, the source and relay either use independent codewords with identical code rates, or different codebooks with different code rates so that the eavesdropper can only decode the two-hop signals individually instead of MRC method. For all the three ATSs, we provide explicit solutions on the optimal system parameters, including the resource allocation between the source and relay, and the code rates. We also present numerical results and comparisons on the secrecy throughput of these schemes.
Nutrition and Growth

Nutrition plays a fundamental role in determining the growth of individuals. An appropriate growth progression is considered a harbinger of adequate nutrient intake and good health. On the other hand growth deceleration with or without short stature may indicate inadequate nutrition, even when there is no body weight deficit for height. Nutritional growth retardation (NGR) is most prevalent in populations at risk of poverty. However in affluent communities patients with NGR are often referred to the specialist because of short stature and delayed sexual development. The diagnosis may be overlooked and/or be established after exhaustive evaluations, if the pattern of weight progression over time is not considered. Patients with so-called idiopathic short stature may present diminished nutrient intake and decreased IGF-I levels, however their nutritional status and body weight progression patterns are usually not addressed by pediatric endocrinologists. NGR patients may cease to gain appropriate weight and fail to grow in height, even without exhibiting body weight deficits for height. They adapt to decreased nutrient intake by decreasing growth progression and thereby achieve equilibrium by decreasing the nutrient demands. This occurs by diminishing their metabolic rates and erythrocyte Na+, K+- ATPase activity, however they may not present alterations in other clinical biochemical markers of malnutrition. Therefore accurate weights and heights plotted on the growth chart over time are necessary to detect NGR. Nutritional rehabilitation is accompanied with catch up growth, though it may be difficult to change the dietary habits of adolescents who exhibit NGR.
Molecular and Physicochemical Characteristics of Fructan during Technological Processing of Agave tequilana Weber var . Azul

Due to the high level of fructans, up to 72% of the dry matter, agave plants (Agavaceae) may be an excellent source to produce pure fructan powders as ingredients in functional food. Reliable analyses about content, quality profile and physicochemical properties are basic requirements for the development of appropriate sequences of processing steps. Samples of agave, harvested after 5-6 years (before flowering), from different plant sections (heart, basic and middle regions of leaves) and from consecutive steps of technological processing were investigated. Content of dry matter, protein and minerals were determined by means of AOAC methods. Content and composition of carbohydrates were analyzed using enzymatic and chromatographic methods. Solubility, viscosity behaviour and stability of solution were studied at different concentrations, pH and temperatures. The structure of fructan was investigated by methylation analysis. 28–32% DM was found in the heart of trunks and in the basic region of leaves. Total amount of carbohydrate was 65–83% of DM (up to 72% of fructan). Protein content was 4.3–5.0% and mineral content was 5.6–6.3% (high level of Ca and Mg). Protein and mineral content was lost during processing. Solubility was approx. 80% with high storage stability. Structure analysis proved agave fructan to be a -(2,1)-linked main chain with a branching degree of 0.22 (22 mol% of alditol derivatives), forming predominantly (2,6)-linkages in the side chains. _____________________________________________________________________________________________________________
Leveraging submetered electricity loads to disaggregate household water-use

The world’s fresh water supply is rapidly dwindling. Informing homeowners of their wateruse patterns can help them reduce consumption. Today’s ‘smart’ meters only show a whole house’s water consumption over time. People need to be able to see where they are using water most to be able to change their habits. The task of inferring the breakdown of wateruse from smart meter data is called water disaggregation. Water disaggregation has been dominated by studies that rely on high-frequency data, proprietary meters, and/or labelled datasets. In contrast, this thesis uses low-frequency data from standardized meters and does not rely on labelled data. To accomplish this, we leverage information from non-intrusive load monitoring, the electricity counterpart of this task. We propose a modification of the Viterbi Algorithm that applies a supervised method to an unsupervised disaggregation problem. Using this, we are able to achieve mean squared errors of under 0.02 L2/min2.
Possible mechanisms of vasorelaxation for 5,7‐dimethoxyflavone from Kaempferia parviflora in the rat aorta

The present study investigated the vascular effects of 5,7‐dimethoxyflavone (DMF), isolated from the rhizomes of Kaempferia parviflora (KP), on rat isolated aortic rings and its possible mechanisms. DMF (1–100 μm) caused concentration‐dependent relaxations in aortic rings precontracted with methoxamine. This effect was significantly reduced by removal of the endothelium, and after pretreatment with NG‐nitro‐L‐arginine methyl ester (L‐NAME, 300 μm), indomethacin (10 μm) and 1H‐[1,2,4]oxadiazolo‐[4,3‐a]quinoxalin‐1‐one (ODQ, 10 μm), but not 9‐(tetrahydro‐2‐furanyl)‐9H‐purine‐6‐amine (SQ22536, 100 μm). Relaxant responses to DMF were significantly inhibited by high KCl (60 mm) in both endothelium‐intact and ‐denuded rings. In addition, the relaxations to DMF were significantly reduced by pretreatment with tetraethylammonium (TEA, 5 mm), glibenclamide (10 μm), 4‐aminopyridine (1 mm) or barium chloride (10 μm). Preincubation with DMF (10 and 100 μm) for 30 min significantly inhibited the contractile responses to CaCl2 in a Ca2+‐free, high K+ buffer. The present study demonstrated that DMF causes endothelium‐dependent relaxation that is partly mediated by NO‐cGMP and cyclooxygenase pathways. Interestingly, DMF‐induced responses are mainly due to increasing K+ efflux, and inhibition of Ca2+ influx from the extracellular space. The vasodilator effects of DMF provide experimental support for the potential use of KP as a medical plant in the treatment of cardiovascular diseases. Copyright © 2010 John Wiley & Sons, Ltd.
A public-domain image processing tool for automated quantification of fluorescence in situ hybridisation signals

Aims: To develop and evaluate an automated method for quantification of HER2 fluorescence in situ hybridisation (FISH) signals. Methods: Using a popular, open source image manipulation tool, ImageJ, a macro for FISH signal assessment was created. A comparison against traditional manual counting was performed in breast cancer specimens from 42 patients. The tumour specimens were hybridised with probes for HER2 and chromosome 17 centromere (CEP17) and selected areas were digitised for image processing. Hybridisation signals were calculated both manually and automatically with the ImageJ custom macro. Results: The correlation coefficient between the automatic and manual HER2/CEP17 ratios was 0.98. The corresponding percentage agreement was 90% and the kappa value was 0.82. Conclusions: This study shows that it is possible to automate the determination of HER2 amplification by the use of open-source software, with results comparable to manual counting. The automated counting decreases the time needed for sample analysis and provides possibilities to enhance inter- and intralaboratory reproducibility of results. The FISH quantification tool (FishJ) is available for download as an ImageJ macro or alternatively it can be utilised through a web interface with an option of uploading FISH images for hybridisation signal counting. Combined with digitisation of FISH samples, the FishJ macro enables gene copy number to be assessed and re-evaluated on any area of a digitised specimen.
Speech polarity detection using strength of impulse-like excitation extracted from speech epochs

In this paper, we address the issue of speech polarity detection using strength of impulse-like excitation around epoch. The correct detection of speech polarity is a crucial step for many speech processing algorithms to extract suitable information. Occurrence of errors in the detection of speech polarity could have an impact on the performance of speech systems. Automatic detection of speech polarity has become an important preliminary step for many speech processing algorithms. We propose a method based on the knowledge of impulse-like excitation of speech production mechanism. The impulse-like excitation is reflected across all frequencies including the zero frequency (0 Hz). Using the slope around zero crossings of the zero frequency filtered signal, an automatic speech polarity detection method is proposed. Performance of the proposed method is demonstrated on 8 different speech corpora. The proposed method is compared with the three existing techniques such as gradient of the spurious glottal waveforms (GSGW), oscillating moments-based polarity detection (OMPD) and residual excitation skewness (RESKEW). From the experimental results, it is observed that the performance of the proposed method is comparable or better than the existing methods for the experiments considered.
Promoting Better Oral Health Practices among Aboriginal Taiwanese Adolescents: A School Based Oral Health Education Intervention Program

The purpose of this study was to test the efficacy of an educational program aimed at improving oral health knowledge and behaviors in junior high school students in indigenous communities in Taiwan. Two junior high schools were randomly selected. Students in the intervention school received an oral health education program. Both groups received structured questionnaires to assess their oral health practices and risk behaviors at baseline and after the intervention. The intervention group had statistically significant positive changes in their oral health knowledge (p<.001), an increase in tooth-brushing frequency (p<.001), and a decrease in tobacco use (p=.01). Most (87%) students considered the educational program excellent or good. Carefully designed health education programs delivered within schools in areas with limited access to health care can improve the students’ knowledge and reduce their risk behaviors which may prove to be a mechanism that ultimately reduces health disparities.
Analysis of the Gene Family Encoding Lipases in Candida rugosa by Competitive Reverse Transcription-PCR

ABSTRACT Synthesis of multiple extracellular lipases in Candida rugosa has been demonstrated. However, it is difficult to characterize the expression spectrum of lip genes, since the sequences of the lip multigene family are very closely related. A competitive reverse transcription-PCR assay was developed to quantify the expression of lip genes. In agreement with the protein profile, the abundance of lip mRNAs was found to be (in decreasing order) lip1, lip3,lip2, lip5, and lip4. To analyze the effects of different culture conditions, the transcript concentrations for these mRNA species were normalized relative to the values for gpd, encoding glyceraldehyde-3-phosphate dehydrogenase. In relative terms, lip1 and lip3were highly and constitutively expressed (about 105molecules per μg of total RNA) whereas the other induciblelip genes, especially lip4, showed significant changes in mRNA expression under different culture conditions. These results indicate that differential transcriptional control oflip genes results in multiple forms of lipase proteins.
Unexpected Diversity of Cellular Immune Responses against Nef and Vif in HIV-1-Infected Patients Who Spontaneously Control Viral Replication

Background HIV-1-infected individuals who spontaneously control viral replication represent an example of successful containment of the AIDS virus. Understanding the anti-viral immune responses in these individuals may help in vaccine design. However, immune responses against HIV-1 are normally analyzed using HIV-1 consensus B 15-mers that overlap by 11 amino acids. Unfortunately, this method may underestimate the real breadth of the cellular immune responses against the autologous sequence of the infecting virus. Methodology and Principal Findings Here we compared cellular immune responses against nef and vif-encoded consensus B 15-mer peptides to responses against HLA class I-predicted minimal optimal epitopes from consensus B and autologous sequences in six patients who have controlled HIV-1 replication. Interestingly, our analysis revealed that three of our patients had broader cellular immune responses against HLA class I-predicted minimal optimal epitopes from either autologous viruses or from the HIV-1 consensus B sequence, when compared to responses against the 15-mer HIV-1 type B consensus peptides. Conclusion and Significance This suggests that the cellular immune responses against HIV-1 in controller patients may be broader than we had previously anticipated.
Spectral-Efficiency Analysis of Regular- and Large-Scale (Massive) MIMO With a Comprehensive Channel Model

This paper provides a generalized analysis for the spectral efficiency of both regular- and large-scale (massive) multiple-input multiple-output (MIMO) systems, where major radio-propagation characteristics and antenna-array parameters are taken into account, including path loss, shadowing effect, multipath fading, antenna correlation, antenna polarization, environmental cross-polarization coupling, and antenna cross-polarization discrimination. After developing the channel model, where the Weichselberger method is exploited to reformulate the Kronecker model and allow closed-form analysis, an upper bound on the spectral efficiency of the MIMO channel is first established, by using the Hadamard's determinant inequality for positive semidefinite matrices. Then, an asymptotic analysis in high signal-to-noise ratio regime is conducted, which explicitly reveals the effects of the aforementioned parameters on the spectral efficiency. Moreover, the asymptotic behavior of the spectral efficiency in the sense of massive MIMO, i.e., as the number of transmit and/or receive antennas approaches infinity, is investigated. Monte Carlo simulation results corroborate the effectiveness of the analysis and the accuracy of the obtained upper bound on the spectral efficiency. Thanks to its high generality, the analysis developed in this paper benefits system designers in the design and performance evaluation of either regular or massive MIMO systems while accounting for realistic phenomena characterizing both the propagation environment and the antenna arrays.
Analysis of the term ‘big data’: Usage in biomedical publications

The meaning of the term “Big Data” is still subject to debate, in spite of being widely used in biomedical publications. This confusion in definition leads to missed opportunities for peers to exchange knowledge and practices. A better understanding of Big Data may help researchers to identify themselves with the Big Data community. In this study, we investigate the most distinguishing features in “Big Data”-labelled publications by comparing them against publication without this label (non-Big Data), using text mining and machine learning methods. Furthermore, the usage of the term Big Data was analysed over time. Our models could successfully make a distinction between publications labelled with ‘Big Data’ and those without. The most distinguishing features consisted of terms such as ‘omics’, ‘computing’, ‘storage’, and ‘mining’. We observed that publications that do not use the term Big Data may also address topics that fall under well-accepted definitions of Big Data. Trends suggest that, while the use of the term Big Data increased, it is used less reliably now as compared to earlier years.