Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytotoxicity and Genotoxicity of Ceria Nanoparticles on Different Cell Lines in Vitro

Owing to their radical scavenging and UV-filtering properties, ceria nanoparticles (CeO2-NPs) are currently used for various applications, including as catalysts in diesel particulate filters. Because of their ability to filter UV light, CeO2-NPs have garnered significant interest in the medical field and, consequently, are poised for use in various applications. The aim of this work was to investigate the effects of short-term (24 h) and long-term (10 days) CeO2-NP exposure to A549, CaCo2 and HepG2 cell lines. Cytotoxicity assays tested CeO2-NPs over a concentration range of 0.5 μg/mL to 5000 μg/mL, whereas genotoxicity assays tested CeO2-NPs over a concentration range of 0.5 μg/mL to 5000 μg/mL. In vitro assays showed almost no short-term exposure toxicity on any of the tested cell lines. Conversely, long-term CeO2-NP exposure proved toxic for all tested cell lines. NP genotoxicity was detectable even at 24-h exposure. HepG2 was the most sensitive cell line overall; however, the A549 line was most sensitive to the lowest concentration tested. Moreover, the results confirmed the ceria nanoparticles’ capacity to protect cells when they are exposed to well-known oxidants such as H2O2. A Comet assay was performed in the presence of both H2O2 and CeO2-NPs. When hydrogen peroxide was maintained at 25 μM, NPs at 0.5 μg/mL, 50 μg/mL, and 500 μg/mL protected the cells from oxidative damage. Thus, the NPs prevented H2O2-induced genotoxic damage.
A Conserved Inverted Repeat, the LipR Box, Mediates Transcriptional Activation of the Streptomyces exfoliatus Lipase Gene by LipR, a Member of the STAND Class of P-Loop Nucleoside Triphosphatases

ABSTRACT Expression of the Streptomyces exfoliatus lipA gene, which encodes an extracellular lipase, depends on LipR, a transcriptional activator that belongs to the STAND class of P-loop nucleoside triphosphatases. LipR is closely related to activators present in some antibiotic biosynthesis clusters of actinomycetes, forming the LipR/TchG family of regulators. In this work we showed that purified LipR protein is essential for activation of lipA transcription in vitro and that this transcription depends on the presence of a conserved inverted repeat, the LipR box, located upstream of the lipA promoter. Mutagenesis of the lipA promoter region indicated that most transcription depends on LipR binding to the proximal half-site of the LipR box in close proximity to the −35 region of the promoter. Our experiments also indicated that LipR establishes contact with the RNA polymerase on both sides of the LipR box, since some activation was observed when only the distal half-site was present or when the entire LipR box was moved further upstream. We also showed that the LipR proteins of S. exfoliatus and Streptomyces coelicolor are functionally interchangeable both in vitro and in vivo, revealing the functional conservation of the regulatory elements in these two species.
The Conceptual Integration Modeling Framework: Abstracting from the Multidimensional Model

Data warehouses are overwhelmingly built through a bottom-up process, which starts with the identification of sources, continues with the extraction and transformation of data from these sources, and then loads the data into a set of data marts according to desired multidimensional relational schemas. End user business intelligence tools are added on top of the materialized multidimensional schemas to drive decision making in an organization. Unfortunately, this bottom-up approach is costly both in terms of the skilled users needed and the sheer size of the warehouses. This paper proposes a top-down framework in which data warehousing is driven by a conceptual model. The framework offers both design time and run time environments. At design time, a business user first uses the conceptual modeling language as a multidimensional object model to specify what business information is needed; then she maps the conceptual model to a pre-existing logical multidimensional representation. At run time, a system will transform the user conceptual model together with the mappings into views over the logical multidimensional representation. We focus on how the user can conceptually abstract from an existing data warehouse, and on how this conceptual model can be mapped to the logical multidimensional representation. We also give an indication of what query language is used over the conceptual model. Finally, we argue that our framework is a step along the way to allowing automatic generation of the data warehouse.
Morphology and Morphogenesis of a Novel Saline Soil Hypotrichous Ciliate, Gonostomum sinicum nov. spec. (Ciliophora, Hypotrichia, Gonostomatidae), Including a Report on the Small Subunit rDNA Sequence

Morphology, cirral pattern, and morphogenesis of the new saline soil hypotrich, Gonostomum sinicum nov. spec. collected from Longfeng Wetland in Daqing, north China, were studied, using detailed live observations and protargol‐stained specimens. The new species is characterized as follows: (i) a size in vivo of 100–125 × 30–40 μm, (ii) colorless cortical granules, 0.5 μm across, arranged in short rows, (iii) an adoral zone composed of 28–33 membranelles, (iv) three or four frontoventral rows, one of which extends onto the postoral area, (v) left and right marginal rows composed of 18–27 and 21–35, cirri, respectively, and (vi) usually two transverse cirri. Morphogenesis is as usual for the genus Gonostomum, i.e. the cirral primordia II–VI are primary primordia which split into two sets for proter and opisthe in division middle stages, except for anlage I which develops independently. However, the number of frontoventral transverse anlagen is either five or six not only in different individuals but even in proter and opisthe of the same divider. The phylogenetic analyses based on SSU rDNA sequences showed that the genus Gonostomum is nonmonophyletic, indicating that the patterns of cirri and dorsal kineties are homoplasious characters. The new species G. sinicum nov. spec. is perhaps closely related to Cotterillia bromelicola and two congeners.
Hole hopping through tyrosine/tryptophan chains protects proteins from oxidative damage

Significance Proteins and enzymes are susceptible to oxidative damage and inactivation from reactive oxygen and nitrogen species formed as a consequence of oxidative stress. They also are at risk from oxidizing intermediates formed during enzymatic turnover. A survey of the protein structural database has revealed that one third of structurally characterized proteins contain chains of redox-active tyrosine and tryptophan residues. These chains can protect proteins from damage by transferring oxidizing equivalents away from critical active site regions and delivering them to surface sites for scavenging. Living organisms have adapted to atmospheric dioxygen by exploiting its oxidizing power while protecting themselves against toxic side effects. Reactive oxygen and nitrogen species formed during oxidative stress, as well as high-potential reactive intermediates formed during enzymatic catalysis, could rapidly and irreversibly damage polypeptides were protective mechanisms not available. Chains of redox-active tyrosine and tryptophan residues can transport potentially damaging oxidizing equivalents (holes) away from fragile active sites and toward protein surfaces where they can be scavenged by cellular reductants. Precise positioning of these chains is required to provide effective protection without inhibiting normal function. A search of the structural database reveals that about one third of all proteins contain Tyr/Trp chains composed of three or more residues. Although these chains are distributed among all enzyme classes, they appear with greatest frequency in the oxidoreductases and hydrolases. Consistent with a redox-protective role, approximately half of the dioxygen-using oxidoreductases have Tyr/Trp chain lengths ≥3 residues. Among the hydrolases, long Tyr/Trp chains appear almost exclusively in the glycoside hydrolases. These chains likely are important for substrate binding and positioning, but a secondary redox role also is a possibility.
Decreased fertility in poor responder women is not related to oocyte morphological status

Introduction In women showing impaired fertility, a decreased response to ovarian stimulation is a major problem, limiting the number of oocytes to be used for assisted reproduction techniques (ART). Despite the several definitions of poor response, it is still a matter of debate whether young poor responder patients also show a decrease in oocyte quality. The objective in this study was to investigate whether poor ovarian response to the superstimulation protocol is accompanied by impaired oocyte quality. Material and methods This study included 313 patients younger than 35 years old, undergoing intracytoplasmic sperm injection. Patients with four or fewer MII oocytes (poor-responder group, PR, n = 57) were age-matched with normoresponder patients (NR, n = 256). Results A higher rate of oocyte retrieval and a trend towards an increase in MII oocyte rate were observed in the NR group when compared to the PR group (71.6 ±1.1% and 74.1 ±1.0% vs. 56.3 ±2.9% and 66.5 ±3.7%; p< 0.0001 and p = 0.056, respectively). A trend toward increased implantation rates was observed in the NR group when compared to the PR group (44 and 24.5 ±2.0% vs. 28.8 and 16.4 ±3.9%; p= 0.0305 and p= 0.0651, respectively). Conclusions Low response to ovarian stimulation is apparently not related to impaired oocyte quality. However, embryos produced from poor responder oocytes show impaired capacity to implant and to carry a pregnancy to term.
Sketching Interfaces: Toward More Human Interface Design

Researchers at University of California, Berkeley and Carnegie Mellon University have designed, implemented, and evaluated SILK (Sketching Interfaces Like Krazy), an informal sketching tool that combines many of the benefits of paper-based sketching with the merits of current electronic tools. With SILK, designers can quickly sketch an interface using an electronic pad and stylus, and SILK recognizes widgets and other interface elements as the designer draws them. Unlike paper-based sketching, however, designers can exercise these elements in their sketchy state. For example, a sketched scroll-bar is likely to contain an elevator or thumbnail, the small rectangle a user drags with a mouse. In a paper sketch, the elevator would just sit there, but in a SILK sketch, designers can drag it up and down, which lets them test component or widget behavior. SILK also supports the creation of storyboards-the arrangement of sketches to show how design elements behave, such as how a dialog box appears when the user activates a button. Storyboards are important because they give designers a way to show colleagues, customers, or end users early on how an interface will behave.
Attenuation of 1310- and 1550-nm laser light through sound dental enamel

Inexpensive laser diodes and fiber-optic technology have revived optical transillumination as a promising diagnostic method for the early detection of dental caries. The principal factor limiting transillumination through dental hard tissue is light scattering in the normal enamel and dentin. Previous studies have shown that the scattering coefficient decreases with increasing wavelength. Therefore, the near-IR region is likely to be well suited for fiber optic transillumination. The objective of this study was to measure the optical attenuation of near-IR light through dental enamel at 1310-nm and 1550-nm. These laser wavelengths are readily available due to their suitability for application to fiber optic communication. In this study the collimated transmission of laser light through polished thin sections of dental enamel for various thickness from 0.1 to 2.5 mm was measured in cuvettes of index matching fluid with n= 1.63. Beer-Lambert plots show that the attenuation coefficients are 3.1+/- 0.17cm-1 and 3.8+/- 0.17cm-1 for 1310-nm and 1550-nm, respectively. This study indicates that near-IR laser wavelengths are well-suited for the transillumination of dental enamel for caries detection since the attenuation through normal tissue is an order of magnitude less than in the visible.
Heart Rate Response to Blood Pressure Variations: Sympathetic Activation versus Baroreflex Response in Patients with End-Stage Renal Disease

Background Continuous systolic blood pressure (SBP) and interbeat intervals (IBI) recordings reveal sequences of consecutive beats in which SBP and heart rate change in opposite direction, representing negative feedback baroreflex mechanisms, as well as sequences in which SBP and heart rate change in the same direction (non-baroreflex), believed to represent feedforward control mechanisms. The present study was undertaken to assess the relationship between baroreflex and non-baroreflex sequences in end stage renal insufficiency. Methodology/Principal Findings Continuous beat-to-beat SBP and IBI monitoring was performed in patients on chronic hemodialysis (HD, n=72), in age-matched patients after renal transplantation (TX, n=41) and healthy (control) individuals (C, n=34). The proportion of baroreflex and nonbaroreflex episodes and the b coefficients (the regression line slope of SBP-IBI correlation) were determined using a newly developed 1 minute sliding window method, the classical sequence technique and the "Z" coefficient method. Analysis using the 1 minute sliding window showed an increased proportion of baroreflex episodes in controls and HD, and predominance of nonbaroreflex episodes in TX. An increased proportion of nonbaroreflex episodes in TX patients relative to HD was also revealed by the "Z" method. Baroreflex and nonbaroreflex b coefficients obtained by all methods were markedly decreased in HD. This alteration was reversed at least partly in TX. In HD, both baroreflex and nonbaroreflex b coefficients were inversely correlated to age and CRP levels; in TX, the nonbaroreflex b coefficient was influenced by the type of calcineurin inhibitor. Conclusion/Significance Renal status affects the contribution of baroreflex and nonbaroreflex mechanisms and the strength of SBP-IBI relationship. The predominant contribution of nonbaroreflex mechanisms in TX may be suggestive of enhanced central sympathetic control. Our data may be relevant for understanding of the pathogenesis and selection of appropriate treatment of post-transplant hypertension.
Living arrangements and mental health in Finland

Background: Non-married persons are known to have poor mental health compared with married persons. Health differences between marital status groups may largely arise from corresponding differences in interpersonal social bonds. However, official marital status mirrors the social reality of persons to a decreasing extent, and living arrangements may be a better measure of social bonds. Little is known about mental health in different living arrangement groups. This study aims to establish the extent and determinants of mental health differences by living arrangement in terms of psychological distress (GHQ) and DSM-IV psychiatric disorders (CIDI). Methods: Data were used from the nationally representative cross sectional health 2000 survey, conducted in 2000–1 in Finland. Altogether 4685 participants (80%) aged 30–64 years were included in these analyses; comprehensive information was available on measures of mental health and living arrangements. Living arrangements were measured as follows: married, cohabiting, living with other(s) than a partner, and living alone. Results: Compared with the married, persons living alone and those living with other(s) than a partner were approximately twice as likely to have anxiety or depressive disorders. Cohabiters did not differ from the married. In men, psychological distress was similarly associated with living arrangements. Unemployment, lack of social support, and alcohol consumption attenuated the excess psychological distress and psychiatric morbidity of persons living alone and of those living with other(s) than a partner by about 10%–50% each. Conclusions: Living arrangements are strongly associated with mental health, particularly among men. Information on living arrangements, social support, unemployment, and alcohol use may facilitate early stage recognition of poor mental health in primary health care.
Creating an online dictionary of abbreviations from MEDLINE.

OBJECTIVE The growth of the biomedical literature presents special challenges for both human readers and automatic algorithms. One such challenge derives from the common and uncontrolled use of abbreviations in the literature. Each additional abbreviation increases the effective size of the vocabulary for a field. Therefore, to create an automatically generated and maintained lexicon of abbreviations, we have developed an algorithm to match abbreviations in text with their expansions. DESIGN Our method uses a statistical learning algorithm, logistic regression, to score abbreviation expansions based on their resemblance to a training set of human-annotated abbreviations. We applied it to Medstract, a corpus of MEDLINE abstracts in which abbreviations and their expansions have been manually annotated. We then ran the algorithm on all abstracts in MEDLINE, creating a dictionary of biomedical abbreviations. To test the coverage of the database, we used an independently created list of abbreviations from the China Medical Tribune. MEASUREMENTS We measured the recall and precision of the algorithm in identifying abbreviations from the Medstract corpus. We also measured the recall when searching for abbreviations from the China Medical Tribune against the database. RESULTS On the Medstract corpus, our algorithm achieves up to 83% recall at 80% precision. Applying the algorithm to all of MEDLINE yielded a database of 781,632 high-scoring abbreviations. Of all the abbreviations in the list from the China Medical Tribune, 88% were in the database. CONCLUSION We have developed an algorithm to identify abbreviations from text. We are making this available as a public abbreviation server at \url[http://abbreviation.stanford. edu/].
Living Arrangements of the Elderly in China and Consequences for Their Emotional Well-being

Abstract: We study the living arrangements and consequences for emotional well-being of the elderly in China using data from a national probability sample survey conducted in 2010, part of the China Family Panel Studies: 14,960 households were included and information was collected for each family member. We study 7,015 people in the sample age sixty and older. We find that, compared to living independently with one’s spouse, elderly respondents living with grown children are less happy, have less life satisfaction, and are more depressed, especially when the spouse is not sharing the household. The negative effects largely disappear when there also are grandchildren in the household although widows and widowers remain more prone to depression. Elderly people living in “generation-skipping” families suffer the same fate as living with adult children but no grandchildren—they are less happy and more depressed and, when not sharing responsibilities with a spouse, less satisfied with life than independent elderly couples. Finally, living alone or living with other relatives results in a significant degradation of emotional health. But the very small fraction of elderly respondents living with non-relatives enjoys the greatest happiness and the least depression.
Use of Drotrecogin alfa (activated) in Older Patients with Severe Sepsis

Drotrecogin alfa (activated) has been approved by the United States Food and Drug Administration for treatment of patients at high risk of death from severe sepsis. Severe sepsis is common, and its occurrence increases dramatically with age. Clinical use data, however, suggest that drotrecogin alfa (activated) may be underused in older patients, possibly due to concern over the drug's anticoagulant effects and perceived high cost. In addition, clinicians often treat older patients less aggressively than younger patients. We reviewed a subgroup analysis of patients aged 75 years and older from a large clinical trial evaluating efficacy and safety of drotrecogin alfa (activated), as well as cost‐effectiveness data from real‐world clinical use of the drug in older patients. We also explored ethical dilemmas of treating older patients with sepsis. Drotrecogin alfa (activated) is safe, effective, and cost‐effective in older patients with severe sepsis and should be considered for elderly intensive care patients who are high risk of death and who have no contraindications to treatment.
The Myxococcus xanthus Developmental Program Can Be Delayed by Inhibition of DNA Replication

ABSTRACT Under conditions of nutrient deprivation, Myxococcus xanthus undergoes a developmental process that results in the formation of a fruiting body containing environmentally resistant myxospores. We have shown that myxospores contain two copies of the genome, suggesting that cells must replicate the genome prior to or during development. To further investigate the role of DNA replication in development, a temperature-sensitive dnaB mutant, DnaBA116V, was isolated from M. xanthus. Unlike what happens in Escherichia coli dnaB mutants, where DNA replication immediately halts upon a shift to a nonpermissive temperature, growth and DNA replication of the M. xanthus mutant ceased after one cell doubling at a nonpermissive temperature, 37°C. We demonstrated that at the nonpermissive temperature the DnaBA116V mutant arrested as a population of 1n cells, implying that these cells could complete one round of the cell cycle but did not initiate new rounds of DNA replication. In developmental assays, the DnaBA116V mutant was unable to develop into fruiting bodies and produced fewer myxospores than the wild type at the nonpermissive temperature. However, the mutant was able to undergo development when it was shifted to a permissive temperature, suggesting that cells had the capacity to undergo DNA replication during development and to allow the formation of myxospores.
Twitter sentiment analysis with different feature extractors and dimensionality reduction using supervised learning algorithms

Twitter is an online micro-blogging platform which allows us to treasure trove about the current circumstance at any juncture in time. In this paper, we analyze the sentiments of huge amount of tweets generated from Twitter users which are stored in Twitter database. We have chosen accuracy as the evaluation criteria of classification methods, namely Naive Bayes and Support Vector Machine. Also we have used unigram and bigram as feature extractors along with Chi2 and Singular Value Decomposition for dimensionality reduction. Through tokenization, having several stages of pre-processing and several combinations of feature vectors and classification methods, we are able to achieve an accuracy of 89.61% when analyzing the sentiment of tweets.