Miracle-dz/UniFAR-FTUs huggingface dataset:
Toxicity of ethylmercury (and Thimerosal): a comparison with methylmercury

Ethylmercury (etHg) is derived from the metabolism of thimerosal (o‐carboxyphenyl‐thio‐ethyl‐sodium salt), which is the most widely used form of organic mercury. Because of its application as a vaccine preservative, almost every human and animal (domestic and farmed) that has been immunized with thimerosal‐containing vaccines has been exposed to etHg. Although methylmercury (meHg) is considered a hazardous substance that is to be avoided even at small levels when consumed in foods such as seafood and rice (in Asia), the World Health Organization considers small doses of thimerosal safe regardless of multiple/repetitive exposures to vaccines that are predominantly taken during pregnancy or infancy. We have reviewed in vitro and in vivo studies that compare the toxicological parameters among etHg and other forms of mercury (predominantly meHg) to assess their relative toxicities and potential to cause cumulative insults. In vitro studies comparing etHg with meHg demonstrate equivalent measured outcomes for cardiovascular, neural and immune cells. However, under in vivo conditions, evidence indicates a distinct toxicokinetic profile between meHg and etHg, favoring a shorter blood half‐life, attendant compartment distribution and the elimination of etHg compared with meHg. EtHg's toxicity profile is different from that of meHg, leading to different exposure and toxicity risks. Therefore, in real‐life scenarios, a simultaneous exposure to both etHg and meHg might result in enhanced neurotoxic effects in developing mammals. However, our knowledge on this subject is still incomplete, and studies are required to address the predictability of the additive or synergic toxicological effects of etHg and meHg (or other neurotoxicants). Copyright © 2013 John Wiley & Sons, Ltd.
Numerical Modeling of Steel Corrosion in Concrete Structures due to Chloride Ion, Oxygen and Water Movement

A comprehensive numerical system is proposed for the attempt to solve the problem of the deterioration of reinforced concrete structures subjected to chloride-induced corrosion. This numerical system was created by combining the physicochemical models related to the migration of corrosion-related substances in concrete, such as chloride ions, oxygen and vapor, and the electrochemical models dealing with the formation of half-cell potential from the viewpoints of macrocell corrosion and corrosion current of RC members under chloride-induced corrosion. Chloride ions concentration, oxygen concentration, water content, current density and the loss of cross-sectional area at any position of the rebar can be calculated by this system.
Solute transport and water content measurements in clay soils using time domain reflectometry

Abstract Clayey and saline soils have been shown to be problematic for time domain reflectometry (TDR) measurements. This study presents some of these problems and discusses solutions to them. Thirteen solute transport experiments were carried out in three undisturbed soil columns of swelling clay soil from Tunisia, labelled S1, S2, and S3 respectively. The columns were collected at three different physiographical regions within a catchment. Water fluxes ranged from 1.2 to 7.2 cm day−1. The large solute transport heterogeneity and large tailing indicated that preferential flow was most pronounced in S1. The preferential flow took place in voids between structural elements and in wormholes. In S3, preferential flow was also evident, but not to the same extent as in S1. In S2, the solute transport was more uniform with little preferential flow. The heterogeneity of the solute transport increased with the water flux in S1 and to a smaller extent in S3, whereas it remained constant in S2. In a previous dye experiment in the field, preferential flow in cracks was observed at those sites where S1 and S3 were collected. In the column experiments, preferential flow in these cracks was less due to the higher initial water content compared to the dye experiments, indicating that the desiccation cracks were closed by the swelling clay.
On all things star-free

We investigate the star-free closure, which associates to a class of languages its closure under Boolean operations and marked concatenation. We prove that the star-free closure of any finite class and of any class of groups languages with decidable separation (plus mild additional properties) has decidable separation. We actually show decidability of a stronger property, called covering. This generalizes many results on the subject in a unified framework. A key ingredient is that star-free closure coincides with another closure operator where Kleene stars are also allowed in restricted contexts.
A Key Marine Diazotroph in a Changing Ocean: The Interacting Effects of Temperature, CO2 and Light on the Growth of Trichodesmium erythraeum IMS101

Trichodesmium is a globally important marine diazotroph that accounts for approximately 60 − 80% of marine biological N2 fixation and as such plays a key role in marine N and C cycles. We undertook a comprehensive assessment of how the growth rate of Trichodesmium erythraeum IMS101 was directly affected by the combined interactions of temperature, pCO2 and light intensity. Our key findings were: low pCO2 affected the lower temperature tolerance limit (Tmin) but had no effect on the optimum temperature (Topt) at which growth was maximal or the maximum temperature tolerance limit (Tmax); low pCO2 had a greater effect on the thermal niche width than low-light; the effect of pCO2 on growth rate was more pronounced at suboptimal temperatures than at supraoptimal temperatures; temperature and light had a stronger effect on the photosynthetic efficiency (Fv/Fm) than did CO2; and at Topt, the maximum growth rate increased with increasing CO2, but the initial slope of the growth-irradiance curve was not affected by CO2. In the context of environmental change, our results suggest that the (i) nutrient replete growth rate of Trichodesmium IMS101 would have been severely limited by low pCO2 at the last glacial maximum (LGM), (ii) future increases in pCO2 will increase growth rates in areas where temperature ranges between Tmin to Topt, but will have negligible effect at temperatures between Topt and Tmax, (iii) areal increase of warm surface waters (> 18°C) has allowed the geographic range to increase significantly from the LGM to present and that the range will continue to expand to higher latitudes with continued warming, but (iv) continued global warming may exclude Trichodesmium spp. from some tropical regions by 2100 where temperature exceeds Topt.
A Novel PI Index and Its Applications to QSPR/QSAR Studies

A novel topological index, PI (Padmakar-Ivan index), is derived in this paper. The index is very simple to calculate and has disseminating power similar to that of the Wiener (W) and the Szeged (Sz) indices. The comprehensive studies show that the proposed PI index correlates highly with W and Sz as well as with physicochemical properties and biological activities of a large number of diversified and complex compounds. The proposed PI index promises to be a useful parameter in the QSPR/QSAR studies. The stability of each model is demonstrated by applying cross-validation test. Furthermore, more favorable comparison with other representative indices such as the Randic index is also made in order to establish the predictive ability of the PI index. The results have shown that in several cases the PI index gave better results.
Probing quantum chaos in many-body quantum systems by the induced dissipation

We theoretically analyze the depletion dynamics of an ensemble of cold atoms in a quasi one-dimensional optical lattice where atoms in one of the lattice sites are subject to decay. Unlike the previous studies of this problem in R. Labouvie, {\em et. al}, Phys. Rev. Lett. {\bf 116}, 235302 (2016) we focus on the case where the system is brought to the chaotic regime, that crucially modifies the depletion dynamics as compared to the regular case. It is shown that depletion of the affected site results in gradual depletion of the neighbouring sites according to $t^{1/3}$ scaling law. We also show that by measuring occupations of the lattice sites one can extract important information on chaotic dynamics of the original conservative system.
Macrophage migration inhibitory factor acts as a neurotrophin in the developing inner ear

This study is the first to demonstrate that macrophage migration inhibitory factor (MIF), an immune system ‘inflammatory’ cytokine that is released by the developing otocyst, plays a role in regulating early innervation of the mouse and chick inner ear. We demonstrate that MIF is a major bioactive component of the previously uncharacterized otocyst-derived factor, which directs initial neurite outgrowth from the statoacoustic ganglion (SAG) to the developing inner ear. Recombinant MIF acts as a neurotrophin in promoting both SAG directional neurite outgrowth and neuronal survival and is expressed in both the developing and mature inner ear of chick and mouse. A MIF receptor, CD74, is found on both embryonic SAG neurons and adult mouse spiral ganglion neurons. Mif knockout mice are hearing impaired and demonstrate altered innervation to the organ of Corti, as well as fewer sensory hair cells. Furthermore, mouse embryonic stem cells become neuron-like when exposed to picomolar levels of MIF, suggesting the general importance of this cytokine in neural development.
Improving Prediction Accuracy for WSN Data Reduction by Applying Multivariate Spatio-Temporal Correlation

This paper proposes a method based on multivariate spatial and temporal correlation to improve prediction accuracy in data reduction for Wireless Sensor Networks (WSN). Prediction of data not sent to the sink node is a technique used to save energy in WSNs by reducing the amount of data traffic. However, it may not be very accurate. Simulations were made involving simple linear regression and multiple linear regression functions to assess the performance of the proposed method. The results show a higher correlation between gathered inputs when compared to time, which is an independent variable widely used for prediction and forecasting. Prediction accuracy is lower when simple linear regression is used, whereas multiple linear regression is the most accurate one. In addition to that, our proposal outperforms some current solutions by about 50% in humidity prediction and 21% in light prediction. To the best of our knowledge, we believe that we are probably the first to address prediction based on multivariate correlation for WSN data reduction.
Transmembrane TNF-dependent uptake of anti-TNF antibodies

ABSTRACT TNF-α (TNF), a pro-inflammatory cytokine is synthesized as a 26 kDa protein, anchors in the plasma membrane as transmembrane TNF (TmTNF), and is subjected to proteolysis by the TNF-α converting enzyme (TACE) to release the 15 kDa form of soluble TNF (sTNF). TmTNF and sTNF interact with 2 distinct receptors, TNF-R1 (p55) and TNF-R2 (p75), to mediate the multiple biologic effects of TNF described to date. Several anti-TNF biologics that bind to both forms of TNF and block their interactions with the TNF receptors are now approved for the treatment of a variety of immune-mediated diseases. Several reports suggest that binding of anti-TNFs to TmTNF delivers an outside-to-inside ‘reverse’ signal that may also contribute to the efficacy of anti-TNFs. Some patients, however, develop anti-TNF drug antibody responses (ADA or immunogenicity). Here, we demonstrate biochemically that TmTNF is transiently expressed on the surface of lipopolysaccharide-stimulated primary human monocytes, macrophages, and monocyte-derived dendritic cells (DCs) and expression of TmTNF on the cell surface is enhanced following treatment of cells with TAPI-2, a TACE inhibitor. Importantly, binding of anti-TNFs to TmTNF on DCs results in rapid internalization of the anti-TNF/TmTNF complex first into early endosomes and then lysosomes. The internalized anti-TNF is processed and anti-TNF peptides can be eluted from the surface of DCs. Finally, tetanus toxin peptides fused to anti-TNFs are presented by DCs to initiate T cell recall proliferation response. Collectively, these observations may provide new insights into understanding the biology of TmTNF, mode of action of anti-TNFs, biology of ADA response to anti-TNFs, and may help with the design of the next generation of anti-TNFs.
Movement Disorders after Stroke in Adults: A Review

Background Movement disorders occur in association with stroke and may have important clinical implications. Methods We reviewed the medical literature regarding the clinical phenomenology, prevalence, localization and etiologic implications, and treatments for movement disorders occurring after stroke in adult patients. Results Movement disorders occur uncommonly after stroke and include both hyperkinetic and parkinsonian conditions. They can occur at the time of stroke or appear as a later manifestation. Stroke lesions are typically due to small vessel cerebrovascular disease in the middle or posterior cerebral artery territory, vessels supplying the basal ganglia. Hemorrhagic lesions are more likely to induce hyperkinetic movements. Movement disorders in the setting of stroke tend to resolve spontaneously over time. Medical and surgical therapies are available to treat the movement problems. Discussion Movement disorders after stroke can be helpful in localizing lesions after stroke, determining the etiology of stroke, may need to be a target for therapy and may importantly influence long term outcome.
Classifying $SL_2$-tilings

Recently there has been significant progress in classifying integer friezes and SL2-tilings. Typically, combinatorial methods are employed, involving triangulations of regions and inventive counting techniques. Here we develop a unified approach to such classifications using the tessellation of the hyperbolic plane by ideal triangles induced by the Farey graph. We demonstrate that the geometric, numeric and combinatorial properties of the Farey graph are perfectly suited to classifying tame SL2-tilings, positive integer SL2-tilings, and tame integer friezes - both finite and infinite. In so doing, we obtain geometric analogues of certain known combinatorial models for tilings involving triangulations, and we prove several new results of a similar type too. For instance, we determine those bi-infinite sequences of positive integers that are the quiddity sequence of some positive infinite frieze, and we give a simple combinatorial model for classifying tame integer friezes, which generalises the classical construction of Conway and Coxeter for positive integer friezes.
PCR and ELISA (VIDAS ECO O157®) Escherichia coli O157:H7 identification in Minas Frescal cheese commercialized in Goiânia, GO

Escherichia coli O157:H7 has been incriminated in food poisoning outbreaks and sporadic cases of hemorrhagic colitis and hemolytic uremic syndrome in many countries. Considering the high susceptibility of Minas Frescal cheese to contamination by E. coli O157:H7, the aim of this study was to determine the occurrence of this pathogen through PCR (Polymerase Chain Reaction) and ELISA (VIDAS ECO O157®, bioMérieux, Lyon, France) test. Thirty cheese samples manufactured by artisan farmhouse producers were collected from open-air markets in Goiânia and thirty from industries under Federal Inspection located in Goiás State which trade their products in supermarkets in Goiânia. E. coli O157:H7 was detected in 6.67% samples collected in open air markets using ELISA, and 23,33% with PCR. The pathogen was not detected in samples from industries under Federal Inspection.
Mapping influenza transmission in the ferret model to transmission in humans

The controversy surrounding 'gain-of-function' experiments on high-consequence avian influenza viruses has highlighted the role of ferret transmission experiments in studying the transmission potential of novel influenza strains. However, the mapping between influenza transmission in ferrets and in humans is unsubstantiated. We address this gap by compiling and analyzing 240 estimates of influenza transmission in ferrets and humans. We demonstrate that estimates of ferret secondary attack rate (SAR) explain 66% of the variation in human SAR estimates at the subtype level. Further analysis shows that ferret transmission experiments have potential to identify influenza viruses of concern for epidemic spread in humans, though small sample sizes and biological uncertainties prevent definitive classification of human transmissibility. Thus, ferret transmission experiments provide valid predictions of pandemic potential of novel influenza strains, though results should continue to be corroborated by targeted virological and epidemiological research. DOI: http://dx.doi. org/10.7554/eLife.07969. 001
On the Relationship Between Musicianship and Contralateral Suppression of Transient-Evoked Otoacoustic Emissions.

BACKGROUND The medial olivocochlear (MOC) efferent reflex that modulates outer hair cell function has been shown to be more robust in musicians versus nonmusicians as evidenced in greater contralateral suppression of transient-evoked otoacoustic emissions (TEOAEs). All previous research comparing musical ability and MOC efferent strength has defined musicianship dichotomously (i.e., high-level music students or professional classical musicians versus nonmusicians). PURPOSE The objective of the study was to further explore contralateral suppression of TEOAEs among adults with a full spectrum of musicianship ranging from no history of musicianship to professional musicians. Musicianship was defined by both self-report and with an objective test to quantify individual differences in perceptual music skills. RESEARCH DESIGN A single-factor between-subjects and correlational research designs were employed. STUDY SAMPLE Forty-five normal-hearing young adults participated. DATA COLLECTION AND ANALYSIS Participants completed a questionnaire concerning their music experience and completed the Brief Profile of Music Perception Skills (PROMS) to quantify perceptual musical skills across multiple musical domains (i.e., accent, melody, tempo, and tuning). TEOAEs were evaluated with 60 dB peak equivalent sound pressure level click stimuli with and without a contralateral 65 dB sound pressure level white noise suppressor. TEOAE suppression was expressed in two ways, absolute TEOAE suppression in dB and a normalized index of TEOAE suppression (i.e., percentage of suppression). RESULTS Participants who considered themselves musicians scored significantly higher on all subscales and total Brief PROMS score (p < 0.05). There was no statistically significant difference between musicians and nonmusicians in absolute TEOAE suppression or percentage of TEOAE suppression (p > 0.05). There were no statistically significant correlations or linear predictive relationships between subscale or total Brief PROMS scores with absolute and percentage of TEOAE suppression (p > 0.05). CONCLUSIONS The findings do not support the notion of a graded enhancement of MOC efferent suppression among adults with varied degrees of musicianship from nonmusicians to professional musicians.
Arginase‐II Induces Vascular Smooth Muscle Cell Senescence and Apoptosis Through p66Shc and p53 Independently of Its l‐Arginine Ureahydrolase Activity: Implications for Atherosclerotic Plaque Vulnerability

Background Vascular smooth muscle cell (VSMC) senescence and apoptosis are involved in atherosclerotic plaque vulnerability. Arginase‐II (Arg‐II) has been shown to promote vascular dysfunction and plaque vulnerability phenotypes in mice through uncoupling of endothelial nitric oxide synthase and activation of macrophage inflammation. The function of Arg‐II in VSMCs with respect to plaque vulnerability is unknown. This study investigated the functions of Arg‐II in VSMCs linking to plaque vulnerability. Methods and Results In vitro studies were performed on VSMCs isolated from human umbilical veins, whereas in vivo studies were performed on atherosclerosis‐prone apolipoprotein E‐deficient (ApoE−/−) mice. In nonsenescent VSMCs, overexpressing wild‐type Arg‐II or an l‐arginine ureahydrolase inactive Arg‐II mutant (H160F) caused similar effects on mitochondrial dysfunction, cell apoptosis, and senescence, which were abrogated by silencing p66Shc or p53. The activation of p66Shc but not p53 by Arg‐II was dependent on extracellular signal‐regulated kinases (ERKs) and sequential activation of 40S ribosomal protein S6 kinase 1 (S6K1)—c‐Jun N‐terminal kinases (JNKs). In senescent VSMCs, Arg‐II and S6K1, ERK‐p66Shc, and p53 signaling levels were increased. Silencing Arg‐II reduced all these signalings and cell senescence/apoptosis. Conversely, silencing p66Shc reduced ERK and S6K1 signaling and Arg‐II levels and cell senescence/apoptosis. Furthermore, genetic ablation of Arg‐II in ApoE−/− mice reduced the aforementioned signaling and apoptotic VSMCs in the plaque of aortic roots. Conclusions Arg‐II, independently of its l‐arginine ureahydrolase activity, promotes mitochondrial dysfunction leading to VSMC senescence/apoptosis through complex positive crosstalk among S6K1‐JNK, ERK, p66Shc, and p53, contributing to atherosclerotic vulnerability phenotypes in mice.
Interactive user interface based on Convolutional Auto-encoders for annotating CT-scans

High resolution computed tomography (HRCT) is the most important imaging modality for interstitial lung diseases, where the radiologists are interested in identifying certain patterns, and their volumetric and regional distribution. The use of machine learning can assist the radiologists with both these tasks by performing semantic segmentation. In this paper, we propose an interactive annotation-tool for semantic segmentation that assists the radiologist in labeling CT scans. The annotation tool is evaluated by six radiologists and radiology residents classifying healthy lung and reticular pattern i HRCT images. The usability of the system is evaluated with a System Usability Score (SUS) and interaction information from the readers that used the tool for annotating the CT volumes. It was discovered that the experienced usability and how the users interactied with the system differed between the users. A higher SUS-score was given by users that prioritized learning speed over model accuracy and spent less time with manual labeling and instead utilized the suggestions provided by the GUI. An analysis of the annotation variations between the readers show substantial agreement (Cohen's kappa=0.69) for classification of healthy and affected lung parenchyma in pulmonary fibrosis. The inter-reader variation is a challenge for the definition of ground truth.
The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression

Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Δ cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice and exposes its N and C domains with putative DNA-binding motifs to the nucleoplasm. Genome-wide chromatin immunoprecipitation–on-chip analyses indicated that Src1 is highly enriched at telomeres and subtelomeric regions of the yeast chromosomes. Our data show that the inner nuclear membrane protein Src1 functions at the interface between subtelomeric gene expression and TREX-dependent messenger RNA export through the nuclear pore complexes.