Miracle-dz/UniFAR-FTUs huggingface dataset:
Chapter 10 Optical biosensors for the detection of food borne pathogens

Contagious illnesses are responsible for approximately 20 million deaths annually in the world [1]. In the US alone, 48 million cases, 128,000 hospitalisations, and 3,000 deaths from food borne diseases were reported in 2011 [2]. Some examples of these bacterial and viral agents are Listeria monocytogenes, Staphylococcus aureus, Salmonella sp, Escherichia coli 0157:H7, Norovirus, Hepatitis A, Hepatitis E, Adenovirus (Enteric), and Rotaviruses [3]. Salmonella is one of the most common bacteria responsible for food borne diseases. Salmonella has over 2,463 serotypes and the most prevalent strains are Salmonella typhimurium and Salmonella enteritidis [5]. Salmonella originates from animal intestines and can end up on beef and poultry by contamination during the process of slaughter. It is also found in other animal derived products namely milk and eggs [4]. Vegetable products can also be contaminated with Salmonella through the industrial process. Salmonellosis is a pathology which involves acute fever, diarrhoea, gastroenteritis, and vomiting. The symptoms usually occur within 6–72 h after ingestion and the disease can last up to 7 days [5]. Gastroenteritis is primarily caused by the typhimurium serotype; there have been 1.3 billion cases of typhimurium gastroenteritis which lead to 3 million reported annual deaths. The mortality rate in advanced countries is approximately 1 percent compared to 24 percent in developed countries. Salmonella enteric infection leads to typhoid fever and is less common compared to typhimurium. As evidenced, 17 million cases which lead to 500,000 annual deaths have been reported [6]. Escherichia coli (E. coli) is a bacterium commonly found in the intestines of warm-blooded animals. Most serotypes of E. coli are harmless with the exception of E. coli O157:H7. The primary sources of E. coli O157:H7 include undercooked poultry, meat, and hamburgers and milk-based products such as cheese and yogurt. Additional sources may consist of contaminated vegetables and water. The clinical symptoms associated with E. coli O157:H7 include severe abdominal pain, bloody
Quantifying Perceptual Image Quality

This paper describes a more efficient paired comparison method that reduces the number of trials necessary for converting a table of paired comparisons into scalar data. Instead of comparing every pair of samples (the complete method), a partial method is used that makes more comparisons between closer samples than between more distant samples. A sorting algorithm is used to efficiently order the samples with paired comparisons, and each comparison is recorded. When the sorting is completed, more trials will have been conducted between closer samples than between distant samples. A regression is used to scale the resulting comparison matrix into a one dimensional perceptual quality estimate.
Exploring stacked main memory architecture for 3D GPGPUs

The tremendous number of threads on general purpose graphic processing units (GPGPUs) poses significant challenges on memory architecture design. 3D stacked main memory architecture atop GPGPU is a potential approach to provide high data communication bandwidth and low access latency to meet the requirement of GPGPUs. In this paper, we explore the performance of 3D GPGPUs with stacked main memory. The experimental results show that the 3D stacked GPGPU can provide up to 124.1% and on average 55.8% performance improvement compared to a 2D GPGPU scheme.
Benefit of surgical treatment of lung metastasis in soft tissue sarcoma.

HYPOTHESIS Patients with pulmonary metastatic soft tissue sarcoma benefit from resection, with long-term cure possible. DESIGN Retrospective medical records review. SETTING Academic tertiary care center. PATIENTS Between January 1, 1991, and December 31, 2002, 61 patients (33 men and 28 women; median age at initial diagnosis, 42 years [age range, 18-74 years]) were surgically treated for pulmonary metastases of soft tissue sarcoma at University Hospital, Hamburg-Eppendorf, Germany. INTERVENTIONS Sternotomy or anterior lateral thoracotomy was performed for metastasectomy, including wedge resection or lobectomy. MAIN OUTCOME MEASURE The effects of clinical and pathologic factors on disease-specific survival were analyzed using the log rank test and a multivariate Cox proportional hazards model. RESULTS Primary tumor size was pT1 in 13 patients and pT2 in 48 patients. The differentiation was high in 7 patients, intermediate in 19 patients, and low in 35 patients. The mean number of resected pulmonary metastatic lesions was 5 (range, 1-48). An anterolateral thoracotomy was performed in 39 patients, and sternotomy in 22 patients. There were no significant postoperative complications that required surgical revision. The perioperative mortality was 0%. At a mean follow-up of 60 months, the mean survival time after metastasectomy was 33 months (range, 2-125 months). The 5-year survival was 25%. The number of resected lung metastatic lesions had no prognostic relevance (P = .37). CONCLUSIONS Patients with lung metastasis from soft tissue sarcomas benefit from surgical excision. This treatment has low complication rates and has a favorable influence on the course of the disease. Long-term survival is possible even when recurrent pulmonary disease is resected.
Cpg Methylation in G-Quadruplex and IMotif DNA Structures

Abberant hypomethylation in DNA regions with noncanonical folding potential (ncDNA motifs) is believed to predetermine tumor development - presumably, by facilitating G-quadruplex (G4) and/or i-motif (IM) formation via altering nucleosome positioning (stable G4s induce subsequent genomic rearrangements). We questioned whether CpG methylation per se affects the dsDNA-ncDNA equilibrium. Thermodynamic studies of genomic and model oligonucleotides with methylated CpG sites at different positions are reported. The genomic oligonucleotides analyzed in this work are DNA fragments with reportedly different methylation statuses in colorectal cancer and normal cells. Free energies of duplex, ncDNA formation from single strands were calculated based on melting curve analyses. Polyethylenglycole was used to imitate crowding effect. Our results suggest that CpG methylation may alter the energetic barrier for dsDNA-IM transitions.
High resilience in robotics with a multi-objective evolutionary algorithm

Damage recovery is critical for autonomous robots that need to operate for a long time without assistance. Most current methods are complex and costly because they require anticipating each potential damage in order to have a contingency plan ready. An alternative line of thought is to let the robot learn on its own the best behavior for the current situation. If the learning process is open enough, then the robot should be able to discover new compensatory behaviors in situations that have not been foreseen by its designers. Classic reinforcement learning algorithms are hard to apply to low-level robotic problems [11], but evolutionary algorithms (EAs) are good candidates to find original solutions because they can optimize in the continuous domain and work on the structure of controllers, for instance by evolving neural networks. When evolving controllers for robots, EAs are reported to require many hundreds of trials on the robot and to last from two to tens of hours (e.g. [5, 12]). These EAs spend most of their running time in evaluating the quality of controllers by testing them on the target robot. Since, contrary to simulation, reality cannot be sped up, their running time can only be improved by finding strategies to evaluate fewer candidate solutions on the robot. By first learning learning a self-model for the robot, then evolving a controller with this simulation, Bongard et al. [1] designed an algorithm for resilience that makes an important step in this direction. Nevertheless, this algorithm has a few important shortcomings. First, actions and models are
Grounded in Practice: Using Interpretive Research to Build Theory

This paper provides guidance for carrying out research using an interpretive framework to build theory of IS practice. The purpose of the paper is to provide an example of (a) factors influencing the choice of interpretive methods, (b) developing a theoretical framework, (c) particulars of data collection and analysis, and (d) an application of evaluative criteria applicable to interpretive research. This paper is different in that the focus is on describing the research process, conceptual issues and the research methods used rather than the findings. This format is important given that there is no accepted general model for communicating interpretive research, and few guidelines exist for conducting the inductive process central to interpretive research.
Joint estimation of dynamic PET images and temporal basis functions using fully 4D ML-EM

A fully 4D joint-estimation approach to reconstruction of temporal sequences of 3D positron emission tomography (PET) images is proposed. The method estimates both a set of temporal basis functions and the corresponding coefficient for each basis function at each spatial location within the image. The joint estimation is performed through a fully 4D version of the maximum likelihood expectation maximization (ML-EM) algorithm in conjunction with two different models of the mean of the Poisson measured data. The first model regards the coefficients of the temporal basis functions as the unknown parameters to be estimated and the second model regards the temporal basis functions themselves as the unknown parameters. The fully 4D methodology is compared to the conventional frame-by-frame independent reconstruction approach (3D ML-EM) for varying levels of both spatial and temporal post-reconstruction smoothing. It is found that using a set of temporally extensive basis functions (estimated from the data by 4D ML-EM) significantly reduces the spatial noise when compared to the independent method for a given level of image resolution. In addition to spatial image quality advantages, for smaller regions of interest (where statistical quality is often limited) the reconstructed time–activity curves show a lower level of bias and a lower level of noise compared to the independent reconstruction approach. Finally, the method is demonstrated on clinical 4D PET data.
Mechanisms of long‐lasting hyperpolarizations underlying slow sleep oscillations in cat corticothalamic networks.

1. To explore the nature of the long‐lasting hyperpolarizations that characterize slow oscillations in corticothalamic circuits in vivo, intracellular recordings were obtained under ketamine‐xylazine anaesthesia from cortical (Cx) cells of the cat precruciate motor cortex, thalamic reticular (RE) cells from the rostrolateral sector, and thalamocortical (TC) cells from the ventrolateral (VL) nucleus. 2. Measurements in the three cell types showed input resistance (Rin) to be highest during the long‐lasting hyperpolarizations that correspond to depth‐positive waves of the cortical EEG. Rin was lowest during the early phase of high‐amplitude depth‐negative EEG waves and increased thereafter until the next cycle of the slow oscillation. 3. Spontaneous long‐lasting hyperpolarizations were compared with those evoked by dorsal thalamic stimulation. Voltage versus current (V‐I) plots showed similar membrane potential (Vm) ranges and slopes for spontaneous and evoked hyperpolarizations in both Cx and RE cells. V‐I plots from TC cells had similar slopes, but Vm during evoked hyperpolarizations was displaced towards more negative values. 4. Intracellular injection of constant hyperpolarizing current in Cx cells increased the amplitude of the initial part of the depolarizing plateau of the slow oscillation, but decreased the amplitude of the last part. 5. These results suggest disfacilitation to be the dominant mechanism in the membrane of cortical and thalamic cells during the spontaneous long‐lasting hyperpolarizations, which shape and synchronize slow oscillations in corticothalamic networks. In Cx and RE cells, the same mechanism underlies thalamically evoked long‐lasting hyperpolarizations. By contrast, evoked responses in TC cells show a strong additional hyperpolarizing factor. We propose that GABAB processes are stronger in TC than in Cx neurones, thus rendering the thalamus an easier target for absence‐type epileptic phenomena through potentiation of thalamic rebound capabilities.
Evaluation and mechanism of ammonia nitrogen removal using sediments from a malodorous river

Malodorous rivers are among the major environmental problems of cities in developing countries. In addition to the unpleasant smell, the sediments of such rivers can act as a sink for pollutants. The excessive amount of ammonia nitrogen (NH3−N) in rivers is the main factor that causes the malodour. Therefore, a suitable method is necessary for sediment disposition and NH3−N removal in malodorous rivers. The sediment in a malodorous river (PS) in Beijing, China was selected and modified via calcination (PS-D), Na+ doping (PS-Na) and calcination–Na+ doping (PS-DNa). The NH3−N removal efficiency using the four sediment materials was evaluated, and results indicated that the NH3−N removal efficiency using the modified sediment materials could reach over 60%. PS-DNa achieved the highest NH3−N removal efficiency (90.04%). The kinetics study showed that the pseudo-second-order model could effectively describe the sorption kinetics and that the exterior activated site had the main function of P sorption. The results of the sorption isotherms indicated that the maximum sorption capacities of PS-Na, PS-D and PS-DNa were 0.343, 0.831 and 1.113 mg g−1, respectively, and a high temperature was favourable to sorption. The calculated thermodynamic parameters suggested that sorption was a feasible or spontaneous (ΔG < 0), entropy-driven (ΔS > 0), and endothermic (ΔH > 0) reaction.
Biotic ligand model of the acute toxicity of metals. 1. Technical Basis

The biotic ligand model (BLM) of acute metal toxicity to aquatic organisms is based on the idea that mortality occurs when the metal—biotic ligand complex reaches a critical concentration. For fish, the biotic ligand is either known or suspected to be the sodium or calcium channel proteins in the gill surface that regulate the ionic composition of the blood. For other organisms, it is hypothesized that a biotic ligand exists and that mortality can be modeled in a similar way. The biotic ligand interacts with the metal cations in solution. The amount of metal that binds is determined by a competition for metal ions between the biotic ligand and the other aqueous ligands, particularly dissolved organic matter (DOM), and the competition for the biotic ligand between the toxic metal ion and the other metal cations in solution, for example, calcium. The model is a generalization of the free ion activity model that relates toxicity to the concentration of the divalent metal cation. The difference is the presence of competitive binding at the biotic ligand, which models the protective effects of other metal cations, and the direct influence of pH. The model is implemented using the Windermere humic aqueous model (WHAM) model of metal—DOM complexation. It is applied to copper and silver using gill complexation constants reported by R. Playle and coworkers. Initial application is made to the fathead minnow data set reported by R. Erickson and a water effects ratio data set by J. Diamond. The use of the BLM for determining total maximum daily loadings (TMDLs) and for regional risk assessments is discussed within a probabilistic framework. At first glance, it appears that a large amount of data are required for a successful application. However, the use of lognormal probability distributions reduces the required data to a manageable amount.
Electric field exposure promotes epithelial-mesenchymal transition in human lens epithelial cells via integrin β1-FAK signaling

Electric field (EF) exposure can affect the elongation, migration, orientation, and division of cells. The present study tested the hypothesis that EF may also affect epithelial-mesenchymal transition (EMT) in lens epithelial cells and that this effect may be an important inducer in the pathological process of posterior capsule opacification (PCO). Human lens epithelial (HLE)-B3 cells were exposed to an EF. Experiments were performed in the presence or absence of an anti-integrin β1 blocking antibody or a small molecule inhibitor targeting focal adhesion kinase (FAK). Cell morphology changes were observed by microscopy. The expression levels of integrin β1, FAK, phosphorylated (p)FAK and of EMT markers, E-cadherin and Vimentin, were examined by immunofluorescence, reverse transcription-quantitative polymerase chain reaction and western blotting. Following exposure to EF, HLE-B3 cells appeared elongated and resembled more fibroblast-like cells. Expression of E-cadherin was decreased, while expression of Vimentin was increased in HLE-B3 cells exposed to EF, compared with control cells. In addition, the mRNA expression levels of integrin β1 were increased, and the protein expression levels of integrin β1 and pFAK were increased in HLE-B3 cells exposed to EF, compared with control cells. Blocking of integrin β1 suppressed the EMT-related morphological changes of HLE-B3 cells and reduced the activation of FAK following EF exposure. However, blocking of pFAK did not affect the EMT status of HLE-B3 cells induced by EF. In conclusion, the present study demonstrated that EF exposure induced EMT in HLE-B3 cells and that this effect may partially be mediated by the activation of integrin β1-FAK signaling. The present results may provide a new mechanistic approach to prevent the development of PCO.
Analysing the attributes of fiducial markers for robust tracking in augmented reality applications

Tracking the position and orientation pose of camera is a critical challenge for different modern applications like augmented reality, robot navigation, robot localisation, and 3D modelling and surveillance systems. Marker-based tracking is the most active technique used for camera pose estimation. For the development of augmented reality applications different marker-based tracking toolkits are available that consists of specific set of fiducial markers. In this paper, various fiducial marker attributes are analysed that helps to increase the accuracy of marker-based tracking in augmented reality applications. Experimental modules are developed to calculate the optimal values for each attribute. The experiments are designed to analyse the marker size, distance between marker and camera, the marker speed along all axis, the environmental brightness, the lighting contrast in the environment and dependency of marker size on tracking distance. Experimental study shows that these attributes affect the marker tracking. Augmented reality researchers can use these findings for the development of more reliable and accurate application.
Chemical composition and biological activities of the essential oil of Laggera aurita Linn (DC.) grown in Pakistan

Aim: Laggera aurita Linn (DC.) (Asteraceae), an aromatic weed, has significant ethno medicinal use in China. This study was designed to determine xanthine oxidase, antioxidant, and antibacterial activities of the steam distilled volatile oil of Laggera aurita grown in Pakistan. Materials and methods: The volatile oil of the aerial parts of L. aurita was obtained by hydrodistillation and analyzed by GC-MS. The biological activities investigated include xanthine oxidase inhibition and antioxidant activities using UV spectrophotometry and antibacterial activity through agar well diffusion method. Results: GC-MS analysis of the steam distilled volatile oil of L. aurita showed highest concentration of fatty acids (47.5%), followed by sesquiterpenes (30.8%) and hydrocarbons (8.6%). Monoterpenes and phenolic derivatives were observed as the minor components. The volatile oil exhibited significant xanthine oxidase inhibition potential with IC 50 =0.45 ± 0.009 mg/ml. A dose-dependent increase in the antioxidant potential was observed in DPPH
Mapping of visuospatial functions during brain surgery: a new tool to prevent unilateral spatial neglect.

To the Editor: In the last decade, major advances in intraoperative functional mapping have dramatically improved the results of brain surgery. When removing a brain tumor, it is common clinical practice to awaken the patient and temporarily inactivate small (approximately 5 mm) brain regions with electrical stimuli, while the patient performs functional tasks. If the patient produces incorrect responses, the surgeon leaves the region intact, to preserve the patient’s functional abilities (3). This procedure allows the surgeon to minimize the residual morbidity while increasing the quality of the resection, and the net result is to improve overall patient survival. However, although sensorimotor and cognitive functions such as language, memory, or calculation have been extensively mapped intraoperatively, visuospatial functions have received less attention. Unilateral spatial neglect (USN) is a dramatic neurological condition resulting from damage affecting the temporoparietal or frontal cortex, or the thalamus or basal ganglia of the right hemisphere (1). Patients with unilateral spatial neglect behave as if the left part of the world does not exist (2). Their functional recovery is poor, and they endure major clinical and social consequences. USN typically results from vascular stroke, but other etiologies are possible. For example, USN was reported after a patient received right inferior parietal cortectomy for intractable epilepsy (4). Although this particular patient recovered from neglect after 2 years, other neurosurgical patients risk suffering from chronic USN as a result of more extensive, corticosubcortical resections, especially as required for cerebral glioma. In a recent series of eight patients who underwent resection of a glioma confined to the right parietal lobe (5), no new USN was clinically observed postoperatively, but there was no formal neuropsychological testing performed, and it is well known that USN may not be apparent at clinical observation (2). To prevent the occurrence of USN in these patients, we propose intraoperative assessment of visuospatial function by asking patients to bisect 20-cm horizontal lines (Fig. 1). If the patient shifts the subjective center more than approximately 6.5 mm rightward (1), then the neurosurgeon leaves the inactivated area untouched. Using this procedure, we were able to avoid postoperative USN in two patients (ages, 27 and 28 years) who underwent resection of low-grade gliomas in the right temporoparietal region (6). These left-handed patients were awakened during surgery because there was functional magnetic resonance imaging evidence of partial language representation in the right hemisphere. Patients gave their informed consent, FIGURE 1. Line bisection tasks performed during brain surgery are simple and feasible. Under test conditions, a 20-cm line (not shown) is presented, aligned to the subjects’ eye axis, in a central position with respect to the patient’s sagittal head plane. The Role of Electrothrombosis in the GDC Technique
Weighted True Path Rule: a multilabel hierarchical algorithm for gene function prediction

The genome-wide hierarchical classiﬁcation of gene functions, using biomolecular data from high-throughput biotechnologies, is one of the central topics in bioinformatics and functional genomics. In this paper we present a multilabel hierarchical algorithm inspired by the “true path rule” that governs both the Gene Ontology and the Functional Catalogue (FunCat). In particular we propose an enhanced version of the True Path Rule (TPR) algorithm, by which we can control the ﬂow of information between the classiﬁers of the hierarchical ensemble, thus allowing to tune the precision/recall characteristics of the overall hierarchical classiﬁcation system. Results with the model organism S. cerevisiae show that the proposed method signiﬁcantly improves on the basic version of the TPR algorithm, as well as on the Hierarchical Top-down and Flat ensembles.