Miracle-dz/UniFAR-FTUs huggingface dataset:
Ionizing Radiation Induces Stemness in Cancer Cells

The cancer stem cell (CSC) model posits the presence of a small number of CSCs in the heterogeneous cancer cell population that are ultimately responsible for tumor initiation, as well as cancer recurrence and metastasis. CSCs have been isolated from a variety of human cancers and are able to generate a hierarchical and heterogeneous cancer cell population. CSCs are also resistant to conventional chemo- and radio-therapies. Here we report that ionizing radiation can induce stem cell-like properties in heterogeneous cancer cells. Exposure of non-stem cancer cells to ionizing radiation enhanced spherogenesis, and this was accompanied by upregulation of the pluripotency genes Sox2 and Oct3/4. Knockdown of Sox2 or Oct3/4 inhibited radiation–induced spherogenesis and increased cellular sensitivity to radiation. These data demonstrate that ionizing radiation can activate stemness pathways in heterogeneous cancer cells, resulting in the enrichment of a CSC subpopulation with higher resistance to radiotherapy.
Alterations in Phospholipid Catabolism in Mycobacterium Tuberculosis LysX Mutant

Mycobacterium tuberculosis lysX mutant, defective for production of lysinylated phosphatidylglycerol, is sensitive to cationic antimicrobial peptides, is not proficient for proliferation in mice lungs, and exhibits altered membrane potential (Maloney et al., 2009). In the present study we show that a lysX complement strain expressing lysX from inducible tet promoter is proficient in restoring lysX phenotypes, confirming that the observed phenotypes are specific to lysX. To evaluate the correlation between changes in membrane potential and lysX activity, we visualized regions of cardiolipin (CL), one of the abundant phospholipids of mycobacteria, by staining with fluorescent dye 10-N-nonyl acridine orange and found that CL is localized as bright spots at septal regions and poles of actively dividing cells, but not in stationary phase cells. lysX mutants were elongated and showed more numerous and brighter CL staining at both mid cell and quarter cell septa, compared with wild type, indicating a defect in the cell division process. Evaluation of 14C-acetic acid incorporation into major phospholipids such as CL, phosphatidylethanolamine (PE), phosphatidylinositol (PI), and their degradation between lysX mutant and its parent revealed differences in the turnover of PE and PI. Our results favor a hypothesis that alterations in phospholipid metabolism could be contributing to changes in membrane potential, hence the observed phenotype of lysX mutant.
PersonalTouch: Improving Touchscreen Usability by Personalizing Accessibility Settings based on Individual User's Touchscreen Interaction

Modern touchscreen devices have recently introduced customizable touchscreen settings to improve accessibility for users with motor impairments. For example, iOS 10 introduced the following four Touch Accommodation settings: 1) Hold Duration, 2) Ignore Repeat, 3) Tap Assistance, and 4) Tap Assistance Gesture Delay. These four independent settings lead to a total of more than 1 million possible configurations, making it impractical to manually determine the optimal settings. We present PersonalTouch, which collects and analyzes touchscreen gestures performed by individual users, and recommends personalized, optimal touchscreen accessibility settings. Results from our user study show that PersonalTouch significantly improves touch input success rate for users with motor impairments (20.2%, N=12, p=.00054) and for users without motor impairments (1.28%, N=12, p=.032).
Gilles de la Tourette Syndrome in the Middle East

In a cohort of five patients from the Middle East with the Gilles de la Tourette syndrome, family history of a tic disorder or the Gilles de la Tourette syndrome was positive in three cases. In one of these there was a multiply affected pedigree spanning six generations. The phenomenology of the syndrome is the same as that described in Western reports. The familial pattern of inheritance and cross-cultural similarity emphasise the biological factors in the aetiology of the syndrome.
Word Sense Disambiguation using Conceptual Density

This paper present a method for the resolution of lexical ambiguity of nouns and its automatic evaluation over the Brown Corpus. The method relies on the use of the wide-coverage noun taxonomy of WordNet and the notion of conceptual distance among concepts, captured by a Conceptual Density formula developed for this purpose. This fully automatic method requires no hand coding of lexical entries, hand tagging of text nor any kind of training process. The results of the experiments have been automatically evaluted against SemCor, the sense-tagged version of the Brown Corpus.
Two-phase simulation-optimization for vendor selection and order allocation in a solar cell manufacturer

Sometimes, government protectionist policies, changes in the economy, etc. can result in a supply-larger-than-demand situation in solar energy supply chains whereby market clearing prices drop dramatically. This study focuses on changing suppliers' order allocations for cost reductions in the stochastic system of solar cell manufacturing in order to generate a cost-effective product which satisfies the end-customer's requirement of efficiency.
Cloning, sequence, and expression of the pantothenate permease (panF) gene of Escherichia coli

Pantothenate permease, the product of the panF gene, catalyzes the sodium-dependent uptake of extracellular pantothenate. The panF gene was isolated from an Escherichia coli genomic DNA library and subcloned into multicopy plasmids. Increased copy number of the panF+ allele resulted in increased rates of pantothenate uptake and a significant increase in the steady-state intracellular pantothenate concentration. Despite the higher levels of pantothenate, the utilization of pantothenate for coenzyme A formation was not elevated, indicating that pantothenate kinase activity is the dominant regulator of coenzyme A biosynthesis. DNA sequencing of the panF gene revealed the presence of a single open reading frame that encoded a hydrophobic protein with a molecular weight of 51,992. Sequence analysis predicts that pantothenate permease is an integral membrane protein possessing 12 hydrophobic membrane-spanning domains connected by short hydrophilic sequences. The predicted topological profile of pantothenate permease is similar to that of other membrane carriers that catalyze cation-dependent symport.
Gain-scheduled H∞ constraint Pareto optimal strategy for stochastic LPV systems with multiple decision makers

Gain-scheduled H∞ constraint Pareto optimal strategy for stochastic linear parameter varying (LPV) systems with multiple decision makers is investigated. The modified stochastic bounded real lemma and linear quadratic control (LQC) for the stochastic LPV systems are reformulated by means of linear matrix inequalities (LMIs). In order to decide the strategy set of multiple decision makers, Pareto optimal strategy is considered for each player and the H∞ constraint is imposed. The solvability conditions of the problem are established from cross-coupled matrix inequalities (CCMIs). The efficiency of the proposed strategy set is demonstrated using a numerical example.
Confidence measures for spontaneous speech recognition

For many practical applications of speech recognition systems, it is desirable to have an estimate of confidence for each hypothesized word, i.e. to have an estimate of which words of the output of the speech recognizer are likely to be correct and which are not reliable. We describe the development of the measure of the confidence tagger JANKA, which is able to provide confidence information for the words at the output of the speech recognizer JANUS-3-SR. On a spontaneous German human-to-human database, JANKA achieves a tagging accuracy of 90% at a baseline word accuracy of 82%.
Indoor pedestrian navigation systems: is more than one landmark needed for efficient self-localization?

Research examining pedestrian navigation systems that use landmarks to explain routes became popular in the past years. Nevertheless, it is still an open question how many landmarks should be depicted at once. In this paper a user study is presented that evaluates two different indoor navigation system designs that depict either one (N = 63) or four (N = 60) landmarks to guide the user. The time it took the participants to recognize where to go was captured as a dependent variable. Results show that the interface only depicting one landmark leads to faster self-localization. Therefore, it is argued that a pedestrian navigation system should mainly depict one highly salient landmark in a navigation instruction in order to keep navigation efficiency high.
Knowledge, Attitude, and Practice of Pesticides Use Among Agricultural Workers

Background: Pesticides have critical effects on human health. Because of the high amount of pesticides used, individual exposure is almost inevitable. According to the above-mentioned issues, few studies have been done in this area in Iran. Therefore, this study was conducted to evaluate the knowledge, attitude, and practice of pesticides use among farmers in Kabudrahang County, Hamadan Province, Iran. Materials and Methods: This cross-sectional study was conducted in Kabudrahang County. Data were collected from 262 farmer's sprayer, during April to July 2016. Data were collected, using convenience sampling through interviews with the farmers who had spryer during period spraying. Data collection instrument was a questionnaire that included three sections. Content validity ratio and content validity index indicators were used to measure the validity of questionnaire used from. Data were recorded in SPSS version 21.0 (SPSS Inc., Chicago, Illinois) and were analyzed using frequency analysis and Pearson correlation test. Results: Burning eyes and dizziness were the greater symptoms of poisoning with pesticides. Overall, most of them did not have proper knowledge. Many farmers had proper attitudes toward the use of personal protective equipment. However, 37.4% of them reported that the use of personal protective equipment is not easy. The farmers' practice toward the use of the personal protective equipment correlated with their knowledge and attitude (P < 0.001). Conclusion: It is proposed that educational sets consisted of acquaintance with poisons and their applications, storage, and carrying the pesticides, the methods for effective of different individual protection facilities, and utilizing the behavior to reduce the exposure to poisons should be developed and be available to farmers.
Slow Robots for Unobtrusive Posture Correction

Prolonged static and unbalanced sitting postures during computer usage contribute to musculoskeletal discomfort. In this paper, we investigated the use of a very slow moving monitor for unobtrusive posture correction. In a first study, we identified display velocities below the perception threshold and observed how users (without being aware) responded by gradually following the monitor's motion. From the result, we designed a robotic monitor that moves imperceptible to counterbalance unbalanced sitting postures and induces posture correction. In an evaluation study (n=12), we had participants work for four hours without and with our prototype (8 in total). Results showed that actuation increased the frequency of non-disruptive swift posture corrections and significantly reduced the duration of unbalanced sitting. Most users appreciated the monitor correcting their posture and reported less physical fatigue. With slow robots, we make the first step toward using actuated objects for unobtrusive behavioral changes.
Association of the Fractal Dimension of Retinal Arteries and Veins with Quantitative Brain MRI Measures in HIV-Infected and Uninfected Women

Objective The fractal dimension of retinal arteries and veins is a measure of the complexity of the vascular tree. We hypothesized that retinal fractal dimension would be associated with brain volume and white matter integrity in HIV-infected women. Design Nested case-control within longitudinal cohort study. Methods Women were recruited from the Brooklyn site of the Women’s Interagency HIV study (WIHS); 34 HIV-infected and 21 HIV-uninfected women with analyzable MRIs and retinal photographs were included. Fractal dimension was determined using the SIVA software program on skeletonized retinal images. The relationship between predictors (retinal vascular measures) and outcomes (quantitative MRI measures) were analyzed with linear regression models. All models included age, intracranial volume, and both arterial and venous fractal dimension. Some models were adjusted for blood pressure, race/ethnicity, and HIV-infection. Results The women were 45.6 ± 7.3 years of age. Higher arterial dimension was associated with larger cortical volumes, but higher venous dimension was associated with smaller cortical volumes. In fully adjusted models, venous dimension was significantly associated with fractional anisotropy (standardized β = -0.41, p = 0.009) and total gray matter volume (β = -0.24, p = 0.03), and arterial dimension with mean diffusivity (β = -0.33,.p = 0.04) and fractional anisotropy (β = 0.34, p = 0.03). HIV-infection was not associated with any retinal or MRI measure. Conclusions Higher venous fractal dimension was associated with smaller cortical volumes and lower fractional anisotropy, whereas higher arterial fractal dimension was associated with the opposite patterns. Longitudinal studies are needed to validate this finding.
Bacterial community assembly in activated sludge: mapping beta diversity across environmental variables

Effect of ecological variables on community assembly of heterotrophic bacteria at eight full‐scale and two pilot‐scale activated sludge wastewater treatment plants (AS‐WWTPs) were explored by pyrosequencing of 16S rRNA gene amplicons. In total, 39 samples covering a range of abiotic factors spread over space and time were analyzed. A core bacterial community of 24 families detected in at least six of the eight AS‐WWTPs was defined. In addition to the core families, plant‐specific families (observed at <50% AS‐WWTPs) were found to be also important in the community structure. Observed beta diversity was partitioned with respect to ecological variables. Specifically, the following variables were considered: influent wastewater characteristics, season (winter vs. summer), process operations (conventional, oxidation ditch, and sequence batch reactor), reactor sizes (pilot‐scale vs. full‐scale reactors), chemical stresses defined by ozonation of return activated sludge, interannual variation, and geographical locations. Among the assessed variables, influent wastewater characteristics and geographical locations contributed more in explaining the differences between AS‐WWTP bacterial communities with a maximum of approximately 26% of the observed variations. Partitioning of beta diversity is necessary to interpret the inherent variability in microbial community assembly and identify the driving forces at play in engineered microbial ecosystem.
Combination Features for Semantic Similarity Measure

Computing the semantic similarity between words is one of the key tasks in many language-based applications. Recent work has focused on using contextual clues for semantic similarity computation. In this paper, we propose a method to the measure semantic similarity between words using plain text contents. It takes into account information attributes (local) and topic information (global) of words to disclose their semantic similarity scores. The method models the representation of a word as a high dimensional vector of word attributes and latent topics. Thus, the semantic similarity between two words is measured by the semantic distance between their respective vectors. We have tested the proposed method on WordSimilarity-353 dataset. The empirical results have shown the combination features contribute to improve the semantic similarity results the dataset in comparison with previous work on the same task using plain text contents.
Diversifying Query Suggestion Results

In order to improve the user search experience, Query Suggestion, a technique for generating alternative queries to Web users, has become an indispensable feature for commercial search engines. However, previous work mainly focuses on suggesting relevant queries to the original query while ignoring the diversity in the suggestions, which will potentially dissatisfy Web users' information needs. In this paper, we present a novel unified method to suggest both semantically relevant and diverse queries to Web users. The proposed approach is based on Markov random walk and hitting time analysis on the query-URL bipartite graph. It can effectively prevent semantically redundant queries from receiving a high rank, hence encouraging diversities in the results. We evaluate our method on a large commercial clickthrough dataset in terms of relevance measurement and diversity measurement. The experimental results show that our method is very effective in generating both relevant and diverse query suggestions.
Neuromyelitis optica spectrum disorders

Objective: To (1) determine the value of the recently proposed criteria of neuromyelitis optica (NMO) spectrum disorder (NMOSD) that unify patients with NMO and those with limited forms (NMO/LF) with aquaporin-4 immunoglobulin G (AQP4-IgG) antibodies; and (2) investigate the clinical significance of the serologic status in patients with NMO. Methods: This was a retrospective, multicenter study of 181 patients fulfilling the 2006 NMO criteria (n = 127) or NMO/LF criteria with AQP4-IgG (n = 54). AQP4-IgG and myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG) antibodies were tested using cell-based assays. Results: Patients were mainly white (86%) and female (ratio 6.5:1) with median age at onset 39 years (range 10–77). Compared to patients with NMO and AQP4-IgG (n = 94), those with NMO/LF presented more often with longitudinally extensive transverse myelitis (LETM) (p < 0.001), and had lower relapse rates (p = 0.015), but similar disability outcomes. Nonwhite ethnicity and optic neuritis presentation doubled the risk for developing NMO compared with white race (p = 0.008) or LETM presentation (p = 0.008). Nonwhite race (hazard ratio [HR] 4.3, 95% confidence interval [CI] 1.4–13.6) and older age at onset were associated with worse outcome (for every 10-year increase, HR 1.7, 95% CI 1.3–2.2). Patients with NMO and MOG-IgG (n = 9) had lower female:male ratio (0.8:1) and better disability outcome than AQP4-IgG-seropositive or double-seronegative patients (p < 0.001). Conclusions: In patients with AQP4-IgG, the similar outcomes regardless of the clinical phenotype support the unified term NMOSD; nonwhite ethnicity and older age at onset are associated with worse outcome. Double-seronegative and AQP4-IgG-seropositive NMO have a similar clinical outcome. The better prognosis of patients with MOG-IgG and NMO suggests that phenotypic and serologic classification is useful.
Evaluation of the atmospheric significance of multiphase reactions in atmospheric secondary organic aerosol formation

Abstract. In a simple conceptual cloud-aerosol model the mass of secondary organic aerosol (SOA) that may be formed in multiphase reaction in an idealized scenario involving two cloud cycles separated with a cloud-free period is evaluated. The conditions are set to those typical of continental clouds, and each parameter used in the model calculations is selected as a mean of available observational data of individual species for which the multiphase SOA formation route has been established. In the idealized setting gas and aqueous-phase reactions are both considered, but only the latter is expected to yield products of sufficiently low volatility to be retained by aerosol particles after the cloud dissipates. The key variable of the model is the Henry-constant which primarily determines how important multiphase reactions are relative to gas-phase photooxidation processes. The precursor considered in the model is assumed to already have some affinity to water, i.e. it is a compound having oxygen-containing functional group(s). As a principal model output an aerosol yield parameter is calculated for the multiphase SOA formation route as a function of the Henry-constant, and has been found to be significant already above H~103 M atm-1. Among the potential precursors that may be eligible for this mechanism based on their Henry constants, there are a suite of oxygenated compounds such as primary oxidation products of biogenic and anthropogenic hydrocarbons, including, for example, pinonaldehyde. Finally, the analogy of multiphase SOA formation to in-cloud sulfate production is exploited.
Host plant genetics affect hidden ecological players: links among Populus, condensed tannins, and fungal endophyte infection

Recent studies have shown effects of host plant genetics on community and ecosystem processes, which makes understanding the impacts of genetically based traits on hidden or non-apparent organisms more important. Here we examined links among genetic variation in hybrid cottonwoods, plant phytochemistry, and twig fungal endophytes (i.e., a common hidden organism). We found three major patterns: (1) twig fungal endophyte infection was positively related to the introgression of Fremont cottonwood (Populus fremontii S. Wats.) RFLP genetic markers, (2) condensed tannin concentration in twig bark tissue was negatively correlated to the introgression of Fremont genetic markers, and (3) fungal endophyte infection was negatively related to condensed tannin concentration in twig bark. These data dem- onstrate that plant genotype can impact hidden ecological players (i.e., fungal endophytes) resulting in community and ecosystem consequences.
Accounting for Companding Nonlinearities in Lossless Audio Compression

This paper introduces a novel prediction structure for improving the lossless compression ratio, by accounting for companding nonlinearities of different sample-based audio formats. This applies to a wide class of formats including a-law, μ-law, DAT-LP (digital audio tape recorders), DV-LP (digital video camcorders), and HDCD (high definition compatible digital). The proposed prediction structure obtains significant compression improvements (8-12%) over traditional linear prediction for a-law, μ-law, DAT-LP, DV-LP and also small compression improvements for HDCD. The improvement in compression can also be used for the detection of nonlinearities in HDCD format, making possible to play HDCD CDs at improved audio resolution in ordinary public domain players.
On the martingale property in the rough Bergomi model

We consider a class of fractional stochastic volatility models (including the so-called rough Bergomi model), where the volatility is a superlinear function of a fractional Gaussian process. We show that the stock price is a true martingale if and only if the correlation $\rho$ between the driving Brownian motions of the stock and the volatility is nonpositive. We also show that for each $\rho \frac{1}{{1-\rho^2}}$, the $m$-th moment of the stock price is infinite at each positive time.