Miracle-dz/UniFAR-FTUs huggingface dataset:
Inhibition by Methylphenidate of Transport Across the Yeast Cell Membrane

The influence of methylphenidate on glycolysis in yeast cells was studied to describe more fully the nature of the reactions in which this drug participates. CO2 production and O2 uptake of yeast cells was inhibited 75% by a 10 mm concentration of the compound. This effect, with glucose as a substrate, occurred at pH 7.0, but not at pH 4.5. Kinetic data indicated that the reaction was noncompetitive and complex; the methylphenidate effect on CO2 production could not readily be reversed. Glycolysis by cell-free extracts was not inhibited at the 10-mm concentration, but was affected at 100 mm. Utilization of O2 with maltose and ethyl alcohol as substrates also was reduced. Entry into the cells of a number of different carbohydrates and of glycine was inhibited to different degrees. The loss from suspended cells of materials absorbing at 280 nm was reduced, and the efflux of sorbose, arabinose, and lactose was decreased. Thus, transport into and out of the cells was inhibited and leakage, or permeability, was reduced. It is hypothesized that methylphenidate reacts with a cell membrane constituent, or constituents, and inhibits glycolysis by blocking sugar passage.
Role of Stress Response Sigma Factor SigG in Mycobacterium tuberculosis

ABSTRACT The sigG gene of Mycobacterium tuberculosis was disrupted by homologous recombination, and the genes regulated by SigG were examined by real-time reverse-transcription PCR and microarray studies. The SigG consensus promoter recognition sequence was identified as GCGNGT-N15-18-CGANCA. A ΔsigG mutant was found to be more resistant to mitomycin C treatment than the wild-type strain, indicating that it may be involved in the SOS response in M. tuberculosis.
A Model-Theoretic Approach to Belief Change in Answer Set Programming

We address the problem of belief change in (nonmonotonic) logic programming under answer set semantics. Our formal techniques are analogous to those of distance-based belief revision in propositional logic. In particular, we build upon the model theory of logic programs furnished by SE interpretations, where an SE interpretation is a model of a logic program in the same way that a classical interpretation is a model of a propositional formula. Hence we extend techniques from the area of belief revision based on distance between models to belief change in logic programs. We first consider belief revision: for logic programs P and Q, the goal is to determine a program R that corresponds to the revision of P by Q, denoted P * Q. We investigate several operators, including (logic program) expansion and two revision operators based on the distance between the SE models of logic programs. It proves to be the case that expansion is an interesting operator in its own right, unlike in classical belief revision where it is relatively uninteresting. Expansion and revision are shown to satisfy a suite of interesting properties; in particular, our revision operators satisfy all or nearly all of the AGM postulates for revision. We next consider approaches for merging a set of logic programs, P1, . , Pn. Again, our formal techniques are based on notions of relative distance between the SE models of the logic programs. Two approaches are examined. The first informally selects for each program Pi those models of Pi that vary the least from models of the other programs. The second approach informally selects those models of a program P0 that are closest to the models of programs P1, . , Pn. In this case, P0 can be thought of as a set of database integrity constraints. We examine these operators with regards to how they satisfy relevant postulate sets. Last, we present encodings for computing the revision as well as the merging of logic programs within the same logic programming framework. This gives rise to a direct implementation of our approach in terms of off-the-shelf answer set solvers. These encodings also reflect the fact that our change operators do not increase the complexity of the base formalism.
Spatial Learning and Localization in Rodents: A Computational Model of the Hippocampus and its Implications for Mobile Robots

The ability to acquire a representation of the spatial environment and the ability to localize within it are essential for successful navigation in a-priori unknown environments. The hippocampal forma tion is believed to play a key role in spatial learning and localization in animals in general and rodents in particular. This paper briefly reviews the relevant neurobiological and cognitive data, and their relation to computational models of spatial learning and localization used in contempo rary mobile robots. It proposes a hippocampal model of spatial learning and localization, and characterizes it using a Kalman filter based tool for information fusion from multiple uncertain sources. The resulting model not only explains neurobiological and behavioral data from rodent experiments, but also allows a robot to learn a place-based metric representation of space and to localize itself in a stochastically optimal manner. The paper presents an algorithmic implementa tion of the model and results of several experiments that demonstrate its capabilities. These include the ability to disambiguate perceptually similar places, scale well with increasing errors, and the automatic acquisition of spatial information at multiple resolutions.
Surfactant protein A, but not surfactant protein D, is an opsonin for influenza A virus phagocytosis by rat alveolar macrophages

Surfactant protein A (SP‐A) and surfactant protein D (SP‐D) are collectins, and both proteins were shown to interact with influenza A virus and alveolar macrophages. However, it is not known whether SP‐A and SP‐D can serve as opsonins for the phagocytosis of influenza A virus by alveolar macrophages. In the present study, we investigated the opsonic activities of SP‐A and SP‐D for phagocytosis of fluorescein isothiocyanate (FITC)‐labeled influenza A (H3N2) virus by rat alveolar macrophages using flow cytometry. SP‐A enhanced the association of the virus with macrophages in a dose‐dependent manner, reaching a maximum at an SP‐A concentration of 60 μg/ml. An approximate threefold increase in association of influenza A virus with alveolar macrophages in the presence of SP‐A over control incubations which contained no SP‐A was observed. Half of the total cell‐associated fluorescence could be quenched as demonstrated using the extracellular quenching dye trypan blue. These results indicate that SP‐A mediates internalization of FITC‐labeled influenza A (H3N2) virus by alveolar macrophages. Removal of the carbohydrate moiety of SP‐A by N‐glycosidase F treatment or cleavage of its sialic acid residues by neuraminidase abolished the enhancement of the phagocytosis of FITC‐labeled influenza A virus by alveolar macrophages. Mannan, a mannose homopolysaccharide known to bind to the carbohydrate‐binding domain of SP‐A, did not affect the SP‐A‐mediated phagocytosis of FITC‐labeled influenza by alveolar macrophages. In contrast, SP‐D neither enhanced the association of FITC‐labeled influenza A virus with alveolar macrophages nor affected the opsonic activity of SP‐A for FITC‐labeled influenza A (H3N2) virus at the SP‐D concentrations tested. It is concluded that SP‐A acts via its sialic acid residues as an opsonin in the phagocytosis of influenza A virus by alveolar macrophages.
Spinal cord restitution following compression injuries in rats

ABSTRACT‐ Spinal cord compression injuries were produced in rats by applying weights to a plate 2.2 × 50 mm in size, placed on the exposed midthoracic dura covering the spinal cord. The influence of force and duration of compression was studied by using 3 different weights, 20, 35 and 50 g, applied for 1, 5 and 10 min. Postoperative neurological function was tested by the inclined plane method and the rats were observed for 3 weeks. Neurological impairment increased with force and duration of compression. It is therefore reasonable to conclude that patients suffering from spiral cord injury should be investigated immediately for signs of persistent cord compression. If this is present, early decompression might be of value, although nothing is known in man concerning the limits of force and duration of compression permitting postoperative neurological recovery.
Lower Bounds and Aggregation in Density Estimation

In this paper we prove the optimality of an aggregation procedure. We prove lower bounds for aggregation of model selection type of M density estimators for the Kullback-Leibler divergence (KL), the Hellinger's distance and the L1-distance. The lower bound, with respect to the KL distance, can be achieved by the on-line type estimate suggested, among others, by Yang (2000a). Combining these results, we state that log M/n is an optimal rate of aggregation in the sense of Tsybakov (2003), where n is the sample size.
Subacute complications during recovery from severe traumatic brain injury: frequency and associations with outcome

Background Medical complications after severe traumatic brain injury (S-TBI) may delay or prevent transfer to rehabilitation units and impact on long-term outcome. Objective Mapping of medical complications in the subacute period after S-TBI and the impact of these complications on 1-year outcome to inform healthcare planning and discussion of prognosis with relatives. Setting Prospective multicentre observational study. Recruitment from 6 neurosurgical centres in Sweden and Iceland. Participants and assessments Patients aged 18–65 years with S-TBI and acute Glasgow Coma Scale 3–8, who were admitted to neurointensive care. Assessment of medical complications 3 weeks and 3 months after injury. Follow-up to 1 year. 114 patients recruited with follow-up at 1 year as follows: 100 assessed, 7 dead and 7 dropped out. Outcome measure Glasgow Outcome Scale Extended. Results 68 patients had ≥1 complication 3 weeks after injury. 3 weeks after injury, factors associated with unfavourable outcome at 1 year were: tracheostomy, assisted ventilation, on-going infection, epilepsy and nutrition via nasogastric tube or percutaneous endoscopic gastroscopy (PEG) tube (univariate logistic regression analyses). Multivariate analysis demonstrated that tracheostomy and epilepsy retained significance even after incorporating acute injury severity into the model. 3 months after injury, factors associated with unfavourable outcome were tracheostomy and heterotopic ossification (Fisher's test), infection, hydrocephalus, autonomic instability, PEG feeding and weight loss (univariate logistic regression). PEG feeding and weight loss at 3 months were retained in a multivariate model. Conclusions Subacute complications occurred in two-thirds of patients. Presence of a tracheostomy or epilepsy at 3 weeks, and of PEG feeding and weight loss at 3 months, had robust associations with unfavourable outcome that were incompletely explained by acute injury severity.
Student Column Demographic Disparities in the Tobacco Retail Environment in Boston: A Citywide Spatial Analysis

Tobacco use is recognized by global authoritative bodies, such as the Oxford Health Alliance, as a leading cause of preventable death in the world. Racial/ethnic minority groups (e.g., black and Hispanic people) as well as individuals of lower socioeconomic status (SES) (e.g., low-income individuals) experience disproportionately elevated rates of tobacco-related morbidity and mortality.1 These disparities may be explained in part by differential geographic access to tobacco products. Existing research has found that neighborhoods with high racial/ethnic minority concentrations and lower SES tend to have a higher density of tobacco retailers.2–12 While informative, most of these studies ignore the spatial techniques that are often necessary when using spatial data, notwithstanding early tobacco retailer demographic disparities research explicitly noting the importance of accounting for spatial autocorrelation in future research.4 Limited research has evaluated demographic disparities in the tobacco retail environment that employed a spatial analytic perspective.2,10,12,13 Findings from some studies suggest that performing spatial regressions was necessary when analyzing demographic disparities in the tobacco retail environment.2,13 Spatial regressions account for spatial autocorrelation explicitly by paying attention to the location and arrangement of neighborhood units, resulting in correct parameter estimates and p-values.14–20 Additionally, most studies measure population composition as a continuous variable. However, there may be threshold effects, whereby categorizing population composition (e.g., 60% of a certain racial/ethnic minority group) might matter in the spatial distribution of tobacco retailers. All of the existing research evaluating demographic disparities in the tobacco retail environment of which we are aware used older demographic data (e.g., from the 2000 U.S. Census). Additional studies are needed to monitor current potential demographic disparities in the tobacco retail environment. Indeed, it is important that studies about demographic disparities in the tobacco retailer environment are conducted frequently because the retail landscape may change constantly in certain geographies. In addition, while a study by Laws et al. gathered data on tobacco outlets from three neighborhoods in Boston, Massachusetts, to examine demographic disparities in the tobacco retail environment,3 the results of the study may not be generalizable to other areas. We evaluated racial/ethnic and socioeconomic disparities in the tobacco retail environment across neighborhoods in Boston, considering threshold effects of neighborhood demographics and employing a spatial analytic perspective with current demographic data.
Gastric emptying: the validity of the paracetamol absorption test adjusted for individual pharmacokinetics

An algorithm for the paracetamol absorption test for gastric emptying, adjusting for individual pharmacokinetics, was recently developed. The aim of the present study was to validate the use of this algorithm. Furthermore, the algorithm was applied to elucidate whether a gastric tube interferes with the rate of gastric emptying. A caloric liquid meal with paracetamol was administered orally to nine healthy volunteers on two separate days. On one occasion, the subjects were intubated with a nasogastric tube and the meal was aspirated from the stomach 45 min after meal intake. The percentage of the meal retained in the stomach at the time of aspiration was determined by analyses of paracetamol in the aspirate and compared with calculations by the algorithm. On the other examination day, the same meal was ingested without tube and aspiration. The median percentage of the meal retained in the stomach at aspiration was 47% (range 33–70%) calculated by the algorithm and 48% (range 23–61%) based on the aspiration data. The correlation between the emptying parameters was r=0.97 (P < 0.001). The median of gastric emptying parameters was similar when the number of samples included in the calculation by the algorithm was reduced, but the range tended to increase. The gastric tube moderately inhibited gastric emptying during the period 20–40 min after meal intake (P < 0.05), but for the period from meal intake until start of aspiration, no inhibition was found. The present study demonstrates that the novel algorithm for the paracetamol absorption test provides valid estimates for gastric emptying.
Mathematical modeling for real epidemics situations. The case of classical swine fever virus

In this work, we describe a model to simulate the spread of withinand between- farms transmission of Classical swine fever virus (CSFV). It is a spatial hybrid model, based on the combination of a stochastic individual based model for between-farm spread with a Susceptible-Infected model for within- farm spread. An important characteristic of this model is the use, as an input, of the information available in real databases. The aim of this model is to quantify the magnitude, duration and risk zones of potential CSFV epidemics to provide support for the decision making process in future CSFV outbreaks. Model parameters and assumptions are provided and an illustration of the model’s results is performed by using available data from the Spanish region of Segovia. The outputs are also compared with those given by another model.
Dynamic Models to Learn Physiological Response to Multimedia Stimuli

We suggest dynamic models to learn and predict physiological responses of video-watching people who are exposed to multimodal stimuli, i.e. visual, aural, text, and haptic. Sliding-window-based and lag-based time-series regression methods are considered as basic dynamic models and tested with audio-based arousal prediction case. We set the Mean Affective Profile (MAP) as the common arousal response indicator of people and did prediction experiment using a database of multimodal response to movies, CogDIEM. Experimental results show that systematic prediction of physiological response may be possible. Lag-based time series regression approach shows significantly better performances than sliding-window-
Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women

SUMMARY In this study, we evaluated the association between high-risk human papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in Nigeria between April and August 2012. Vaginal bacterial composition was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV genotyping test. We used exact logistic regression models to evaluate the association between community state types (CSTs) of vaginal microbiota and hrHPV infection, weighted UniFrac distances to compare the vaginal microbiota of individuals with prevalent hrHPV to those without prevalent hrHPV infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants; CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in 7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection and a decreased abundance of Lactobacillus sp. with increased abundance of anaerobes particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P < 0·05). These results are hypothesis generating and further studies are required.
Induction of Vascular Insulin Resistance and Endothelin-1 Expression and Acceleration of Atherosclerosis by the Overexpression of Protein Kinase C-&bgr; Isoform in the Endothelium

Rationale: Loss of insulin action in the endothelium can cause endothelial dysfunction and atherosclerosis. Hyperglycemia and elevated fatty acids induced by diabetes mellitus can activate protein kinase C-&bgr; isoforms and selectively inhibit insulin signaling via phosphatidylinositol 3-kinase/Akt pathway to inhibit the activation of endothelial nitric oxide synthase and metabolic actions. Objective: To demonstrate that overexpressing protein kinase C-&bgr;2 isoform in endothelial cells can cause selective insulin resistance and exacerbate atherosclerosis in the aorta. Methods and Results: Protein kinase C-&bgr;2 isoform was overexpressed in endothelial cells using a promoter of vascular endothelial cell cadherin. These mice were cross-bred with apoE−/− mice [Tg (Prkcb)apoE−/−]. On a Western diet, Tg(Prkcb)apoE−/− and apoE−/− mice did not differ in systemic insulin sensitivity, glucose tolerance, plasma lipid, or blood pressure. Insulin action in endothelial cells and femoral artery from Tg(Prkcb)apoE−/− mice was impaired by ≈40% with respect to Akt/endothelial nitric oxide synthase activation, and leukocyte-endothelial cell binding increased in cultured lung endothelial cells from Tg(Prkcb)apoE−/− mice compared with that from apoE−/− mice. Basal and angiotensin-stimulated big endothelin-1 levels were elevated in Tg(Prkcb)apoE−/− mice compared with apoE−/− mice. The severity of atherosclerosis in the aorta from Tg(Prkcb)apoE−/− mice increased by ≈70% as measured by en face fat staining and plaque content of the number of smooth muscle cells, macrophages, and extracellular matrix. Conclusions: Specific protein kinase C-&bgr;2 activation in the endothelial cells caused dysfunction and accelerated atherosclerosis because of loss of insulin-stimulated Akt/endothelial nitric oxide synthase activation and angiotensin-induced increases in endothelin-1 expression.
Synchronic variation in the articulation and the acoustics of the Polish three-way place distinction in sibilants and its implications for diachronic change

The aim of the present study was to relate articulatory properties of the Polish sibilants /s ʂ ɕ/ to a potential neutralization of /ʂ/ as either /s/ or /ɕ/, the former having occurred in a number of Polish dialects. For this purpose tongue tip (TT) movement data was obtained together with acoustic data using electromagnetic articulography. The sibilants, that were always followed by either /a e o/, were produced by four L1-Polish speakers at fast and slow speech rates. While /s ʂ/ had almost identical transitions, they differed greatly in the spectral characteristics with /ʂ/ being closer to /ɕ/. In order to capture differences in tongue position as well as shape both TT position and TT orientation data were analyzed. The vertical TT orientation showed similarities in /ʂ/ and /s/ production, but the two sibilants were clearly separated in TT position, with /ʂ/ being produced far more back than /s/ and /ɕ/, and the latter two being very similar. The tendentially greater effect of speech rate on /ʂ/ together with the varying acoustic and articulatory similarities between the sibilants are taken as an indicator for greater instability of /ʂ/. This synchronic instability is discussed in terms of potential diachronic mergers.