Miracle-dz/UniFAR-FTUs huggingface dataset:
Adsorption-desorption noise in nanowire FET biosensors

The adsorption-desorption (AD) noise in nanowire FET biosensors is analyzed, which manifests itself in the form of gate voltage fluctuations resulting from the fluctuations of the number of adsorbed particles. The derived theoretical model of the fluctuations takes into account the mass transfer effects. The numerical calculations show that when the mass transfer is slow, the low-frequency amplitude and the corner frequency of the Lorentzian AD noise spectrum obtained by derived expressions are significantly different compared to the same parameters predicted by the model that neglects mass transport effects. The presented analysis enables good estimation of these parameters from the measured noise spectrum, which is important because they are used as the source of information about the analyte concentration and the kinetics of biomolecular interactions.
Pulmonary Wegener's Granulomatosis: A Clinical and Imaging Study of 77 Cases

We studied 77 patients with biopsy-proven WG and pulmonary manifestations, to characterize the nature and frequency of the clinical, imaging and endoscopic features of this condition. Pulmonary symptoms were cough, mild dyspnea, hemoptysis and chest pain. Five patients had no pulmonary symptoms. Imaging features consisted of nodules, infiltrates and pleural opacities. A CT scan proved useful by disclosing cavities in opacities or opacities which were not seen on an x-ray film. Fiberoptic bronchoscopy was performed in 74 patients, and it was macroscopically abnormal in 55 percent (showing bronchial inflammation or stenosis or both or isolated hemorrhage). Six patients presented with alveolar hemorrhagic syndrome. Four patients had a pleural exudate rich in polymorphonuclear leukocytes. The WG was limited to the lung in seven patients. Sixteen patients died because of active disease or iatrogenic complications (two). An improved knowledge of clinical and imaging features of WG could help the clinician reach an earlier diagnosis.
Utilizing Physical Objects and Metaphors for Human Robot Interaction

Mouse, keyboard and graphical user interfaces are commonly used in the field of human-robot interaction (HRI) for robot control. Although these traditional user interfaces (UI) are being accepted as the standard for the majority of computational tasks, their generic nature and interaction styles may not offer ideal mapping to various robotic tasks, such as locomotion and navigation. In our research we intend to explore alternative UIs that could take advantage of human innate skills of physical object manipulation and spatial perception, and overcome some of the problems associated with traditional UIs. We suggest the use of tangible user interfaces (TUIs) for HRI applications, leveraging on existing and well-learned physical metaphors for interaction with robots, and exploring new ways to tangibly control one-to-many robot group interaction tasks. In this paper we will describe our current research efforts and findings, and outline our proposed research plans.
Molecular tumor board: the University of California-San Diego Moores Cancer Center experience.

OBJECTIVE DNA sequencing tests are enabling physicians to interrogate the molecular profiles of patients' tumors, but most oncologists have not been trained in advanced genomics. We initiated a molecular tumor board to provide expert multidisciplinary input for these patients. MATERIALS AND METHODS A team that included clinicians, basic scientists, geneticists, and bioinformatics/pathway scientists with expertise in various cancer types attended. Molecular tests were performed in a Clinical Laboratory Improvement Amendments environment. RESULTS Patients (n = 34, since December 2012) had received a median of three prior therapies. The median time from physician order to receipt of molecular diagnostic test results was 27 days (range: 14-77 days). Patients had a median of 4 molecular abnormalities (range: 1-14 abnormalities) found by next-generation sequencing (182- or 236-gene panels). Seventy-four genes were involved, with 123 distinct abnormalities. Importantly, no two patients had the same aberrations, and 107 distinct abnormalities were seen only once. Among the 11 evaluable patients whose treatment had been informed by molecular diagnostics, 3 achieved partial responses (progression-free survival of 3.4 months, ≥6.5 months, and 7.6 months). The most common reasons for being unable to act on the molecular diagnostic results were that patients were ineligible for or could not travel to an appropriately targeted clinical trial and/or that insurance would not cover the cognate agents. CONCLUSION Genomic sequencing is revealing complex molecular profiles that differ by patient. Multidisciplinary molecular tumor boards may help optimize management. Barriers to personalized therapy include access to appropriately targeted drugs.
Applying random projection to the classification of malicious applications using data mining algorithms

This research is part of a continuing effort to show the viability of using random projection as a feature extraction and reduction technique in the classification of malware to produce more accurate classifiers. In this paper, we use a vector space model with n-gram analysis to produce weighted feature vectors from binary executables, which we then reduce to a smaller feature set using the random projection method proposed by Achlioptas, and the feature selection method of mutual information to produce two separate data sets. We then apply several popular machine learning algorithms including J48 decision tree, naïve Bayes, support vector machines, and an instance-based learner to the data sets to produce classifiers for the detection of malicious executables. We evaluate the performance of the different classifiers and discover that using a data set reduced by random projection can improve the performance of support vector machine and instance-based learner classifiers.
Type II Diacylglycerol Acyltransferase from Claviceps purpurea with Ricinoleic Acid, a Hydroxyl Fatty Acid of Industrial Importance, as Preferred Substrate

ABSTRACT Claviceps purpurea, the fungal pathogen that causes the cereal disease ergot, produces glycerides that contain high levels of ricinoleic acid [(R)-12-hydroxyoctadec-cis-9-enoic acid] in its sclerotia. Recently, a fatty acid hydroxylase (C. purpurea FAH [CpFAH]) involved in the biosynthesis of ricinoleic acid was identified from this fungus (D. Meesapyodsuk and X. Qiu, Plant Physiol. 147:1325-1333, 2008). Here, we describe the cloning and biochemical characterization of a C. purpurea type II diacylglycerol acyltransferase (CpDGAT2) involved in the assembly of ricinoleic acid into triglycerides. The CpDGAT2 gene was cloned by degenerate RT-PCR (reverse transcription-PCR). The expression of this gene restored the in vivo synthesis of triacylglycerol (TAG) in the quadruple mutant strain Saccharomyces cerevisiae H1246, in which all four TAG biosynthesis genes (DGA1, LRO1, ARE1, and ARE2) are disrupted. In vitro enzymatic assays using microsomal preparations from the transformed yeast strain indicated that CpDGAT2 prefers ricinoleic acid as an acyl donor over linoleic acid, oleic acid, or linolenic acid, and it prefers 1,2-dioleoyl-sn-glycerol over 1,2-dipalmitoyl-sn-glycerol as an acyl acceptor. The coexpression of CpFAH with CpDGAT2 in yeast resulted in an increased accumulation of ricinoleic acid compared to the coexpression of CpFAH with the native yeast DGAT2 (S. cerevisiae DGA1 [ScDGA1]) or the expression of CpFAH alone. Northern blot analysis indicated that CpFAH is expressed solely in sclerotium cells, with no transcripts of this gene being detected in mycelium or conidial cells. CpDGAT2 was more widely expressed among the cell types examined, although expression was low in conidiospores. The high expression of CpDGAT2 and CpFAH in sclerotium cells, where high levels of ricinoleate glycerides accumulate, provided further evidence supporting the roles of CpDGAT2 and CpFAH as key enzymes for the synthesis and assembly of ricinoleic acid in C. purpurea.
Risk Factors for Infection or Colonization with CTX-M Extended-Spectrum-β-Lactamase-Positive Escherichia coli

ABSTRACT There has been a significant increase in the prevalence of Enterobacteriaceae that produce CTX-M-type extended-spectrum β-lactamases. The objective of this study was to evaluate risk factors for infection or colonization with CTX-M-positive Escherichia coli. A case-control study was conducted within a university system from 1 January 2007 to 31 December 2008. All patients with clinical cultures with E. coli demonstrating resistance to extended-spectrum cephalosporins were included. Case patients were designated as those with cultures positive for CTX-M-positive E. coli, and control patients were designated as those with non-CTX-M-producing E. coli. Multivariable logistic regression analyses were performed to evaluate risk factors for CTX-M-positive isolates. A total of 83 (56.8%) of a total of 146 patients had cultures with CTX-M-positive E. coli. On multivariable analyses, there was a significant association between infection or colonization with CTX-M-type β-lactamase-positive E. coli and receipt of piperacillin-tazobactam in the 30 days prior to the culture date (odds ratio [OR], 7.36; 95% confidence interval [CI], 1.61 to 33.8; P = 0.01) and a urinary culture source (OR, 0.36; 95% CI, 0.17 to 0.77; P = 0.008). The rates of resistance to fluoroquinolones were significantly higher in isolates from case patients than in isolates from control patients (90.4 and 50.8%, respectively; P < 0.001). We found that nonurinary sources of clinical cultures and the recent use of piperacillin-tazobactam conferred an increased risk of colonization or infection with CTX-M-positive E. coli. Future studies will need to focus on outcomes associated with infections due to CTX-M-positive E. coli, as well as infection control strategies to limit the spread of these increasingly common organisms.
Ice-shelf collapse from subsurface warming as a trigger for Heinrich events

Episodic iceberg-discharge events from the Hudson Strait Ice Stream (HSIS) of the Laurentide Ice Sheet, referred to as Heinrich events, are commonly attributed to internal ice-sheet instabilities, but their systematic occurrence at the culmination of a large reduction in the Atlantic meridional overturning circulation (AMOC) indicates a climate control. We report Mg/Ca data on benthic foraminifera from an intermediate-depth site in the northwest Atlantic and results from a climate-model simulation that reveal basin-wide subsurface warming at the same time as large reductions in the AMOC, with temperature increasing by approximately 2 °C over a 1–2 kyr interval prior to a Heinrich event. In simulations with an ocean model coupled to a thermodynamically active ice shelf, the increase in subsurface temperature increases basal melt rate under an ice shelf fronting the HSIS by a factor of approximately 6. By analogy with recent observations in Antarctica, the resulting ice-shelf loss and attendant HSIS acceleration would produce a Heinrich event.
User perception of interruptions in multimedia annotation tasks

For mixed-initiative multimedia annotation systems an effective dialogue between the system and user is critical. In order to inform the development of such dialogue a clear insight into the impact of interruptions upon the perceptions of the user is required. We present preliminary results of an investigation into interruptions in the form of queries to the user. We show that a user can perceive differences between trivial and important queries. Whether a query is shown in or out of context, or at some opportune time, is also shown to have an impact on user perception of the system.
Forebrain Ischemia Triggers GABAergic System Degeneration in Substantia Nigra at Chronic Stages in Rats

The long-term consequences of forebrain ischemia include delayed Parkinson's syndrome. This study revealed delayed neurodegeneration in the substantia nigra 8 weeks after 12.5 minutes of global ischemia in rat brain. Following neuronal loss of 30–40% in central and dorsolateral striatum at day 3, neuronal damage in the substantia nigra (SN) was assessed at 4–8 weeks using immunohistochemistry for glutamate decarboxylase 67 (GAD67), vesicular GABA transporter (VGAT), and calretinin (CR). At day 56, the optical density of GAD67-, but not VGAT-, immunoreactivity in substantia nigra pars reticulata (SNR)—significantly decreased. CR-neurons concentrated in substantia nigra pars compacta (SNC) were reduced by 27% from day 3 (n = 5) to day 56 (n = 7, ANOVA, p < .01). Movement coordination was impaired at day 56, as evaluated using beam-walking test (time-to-traverse 5.6 ± 1.2 sec versus 11.8 ± 5.4 sec; sham versus ischemia, p < .05, n = 5, and 7, resp.). Our results demonstrate delayed impairment of the GABAergic system components in SN and associated with movement deficits after global ischemia.
Simulated sunlight inactivation of norovirus and FRNA bacteriophage in seawater

To investigate norovirus (NoV) and F‐specific RNA (FRNA) bacteriophage inactivation in seawater under simulated sunlight and temperature conditions representative of summer (235 W m−2; 17°C) and winter (56 W m−2; 10°C) conditions in Ireland.
Chainspace: A Sharded Smart Contracts Platform

Chainspace is a decentralized infrastructure, known as a distributed ledger, that supports user defined smart contracts and executes user-supplied transactions on their objects. The correct execution of smart contract transactions is verifiable by all. The system is scalable, by sharding state and the execution of transactions, and using S-BAC, a distributed commit protocol, to guarantee consistency. Chainspace is secure against subsets of nodes trying to compromise its integrity or availability properties through Byzantine Fault Tolerance (BFT), and extremely high-auditability, non-repudiation and `blockchain' techniques. Even when BFT fails, auditing mechanisms are in place to trace malicious participants. We present the design, rationale, and details of Chainspace; we argue through evaluating an implementation of the system about its scaling and other features; we illustrate a number of privacy-friendly smart contracts for smart metering, polling and banking and measure their performance.
Does training on behavioral finance influence fund managers' perception and behavior?

This paper provides survey evidence on the influence of training on behavioral finance on professional fund managers' perception and investment behavior. In particular, it examines whether "trained" fund managers differ from the "untrained" ones in their perception of markets and themselves as well as in their choice of information sources and investment strategies. Additionally, the influence of integration of behavioral finance approaches into investment processes is also considered. The results reveal that training on behavioral finance basically intensifies the perception of biases in the behavior of others, i.e. the reflection effect and the home bias. Training also reduces the affinity to conformity, leading to less reliance on colleagues and other market participants as information sources. However, pure training is insufficient to significantly affect fund managers' investment behavior, but behavioral finance approaches need to be integrated into investment processes.
Identification of RNA recognition elements in the Saccharomyces cerevisiae transcriptome

Post-transcriptional regulation of gene expression, including mRNA localization, translation and decay, is ubiquitous yet still largely unexplored. How is the post-transcriptional regulatory program of each mRNA encoded in its sequence? Hundreds of specific RNA-binding proteins (RBPs) appear to play roles in mediating the post-transcriptional regulatory program, akin to the roles of specific DNA-binding proteins in transcription. As a step toward decoding the regulatory programs encoded in each mRNA, we focused on specific mRNA–protein interactions. We computationally analyzed the sequences of Saccharomyces cerevisiae mRNAs bound in vivo by 29 specific RBPs, identifying eight novel candidate motifs and confirming or extending six earlier reported recognition elements. Biochemical selections for RNA sequences selectively recognized by 12 yeast RBPs yielded novel motifs bound by Pin4, Nsr1, Hrb1, Gbp2, Sgn1 and Mrn1, and recovered the known recognition elements for Puf3, She2, Vts1 and Whi3. Most of the RNA elements we uncovered were associated with coherent mRNA expression changes and were significantly conserved in related yeasts, supporting their functional importance and suggesting that the corresponding RNA–protein interactions are evolutionarily conserved.
Comparison of Contemporary Technology Acceptance Models and Evaluation of the Best Fit for Health Industry Organizations.

An elaborate literature review was conducted in the area of technology acceptance identifying seminal authors and their views. Several models were examined and three out of theses were chosen based on the popularity in the health care industry. The findings will be presented in this paper, organized in two sections. The first part starts with brief definitions of basic terminology, descriptions and categorization of technology acceptance models. The three most popular contemporary technology acceptance models- (a) Technology Acceptance Model (TAM), (b) Diffusion of Innovation Theory (DOI), and (c) the Unified Theory of Acceptance and Use of Technology (UTAUT) are introduced here to lay the groundwork before they are compared and contrasted, which in turn forms the foundation for the second section. The second part delves into the evaluation of these three contemporary technology acceptance models. Literature in the area of technology acceptance in health care was examined to find the model that best fits in the health care industry.
Strategic entrepreneurship, resource orchestration and growing spin-offs from universities

By combining the strategic entrepreneurship perspective and resource orchestration theory we provide an integrated framework that explains the heterogeneity of growth across different types of university spin-offs (USOs). We show that appropriate resource accumulation, the bundling of resources to build competencies and the leveraging of those competencies into the market are all necessary but they also need to be synchronised with an appropriate growth strategy to realise sustainable growth. We discuss the differential resource needs at different stages of growth as USOs attempt to overcome critical junctures of entrepreneurial commitment and venture credibility. We explain the difficulties of accumulating an appropriate breadth of resources and competencies as they are contingent upon whether the USO should be aiming to sell their technology outright or whether they should be developing a product for a specific market opportunity. We conclude by proposing that universities and technology transfer offices should synchronise the depth of their organisational support to meet the growth contingencies of the USO.
Analysis of phase-matching for the internal second-harmonic generation in InGaAs quantum-well laser diodes emitting around 980 nm

In this paper we report theoretical and experimental results concerning the realization of the phase-matching conditions for the internal second-harmonic generation in InGaAs quantum-well laser diodes emitting around 980 nm in order to enhance the conversion efficiency. The role of the phase-mismatching in the spectral distribution of the internal second-harmonic generation in the CW operation of the above-mentioned lasers is also analyzed. The emission of pairs of narrow blue-green peaks having perfectly symmetrical spectral positions with respect to the central peak of pure second-harmonic generation at ~ 480 nm is most probably enhanced by a mechanism of reciprocal cancellation of the respective phase-mismatch vectors. The theoretical results obtained by numerical integration of the coupled amplitude equations corresponding to the fundamental and second harmonic concerning the interaction length and generation efficiency are in good agreement with the experimental data. The obtained results are important for the assessment of the relationship between the structural parameters of the laser and the conditions which contribute to the stimulation of second-order optical nonlinearities in the laser active region.
The burden of hypertension and diabetes mellitus in rural communities in southern Nigeria

Introduction The African region of the world is experiencing a double epidemic of both communicable and non-communicable diseases. The objective of the study was to determine the prevalence of hypertension and diabetes mellitus among adult residents of rural communities in southern Nigeria. Methods A community based descriptive cross-sectional study. Adults aged 18 years and above residing in the rural communities who attended a free medical outreach programme were screened for hypertension and diabetes mellitus. Data were collected using a structured interviewer-administered questionnaire. Results Of the 845 participants, 349 (41.3%) were aged 50-69 years, 263 (31.1%) were males, and 305 (36.1%) were farmers. Overweight and obesity were found in 184 (21.8%) and 90 (10.6%) of them respectively. The overall prevalence of hypertension was 37.6% (males 43.7%, females 35.1%, p = 0.018) while that of diabetes mellitus was 4.6% (males 1.9%, females 5.8%, p = 0.012). Predictors of hypertension were age ≥ 40 years (OR = 5.04, CI: 2.99 - 8.48), overweight/obesity (OR = 1.56, CI: 1.15 - 2.13) while females are less likely to develop hypertension (OR = 0.72, CI: 0.53 - 0.98). The significant predictor of diabetes mellitus was overweight/obesity (OR = 3.53, CI: 1.78 - 6.98). Conclusion The rising prevalence of hypertension and diabetes mellitus is assuming an epidemic level in rural communities in southern Nigeria. There is an urgent need for intensive health education and community surveillance programmes targeted at rural communities in order to achieve prevention and control of these non-communicable diseases in Nigeria.