Miracle-dz/UniFAR-FTUs huggingface dataset:
Detection of gyrA gene mutations associated with ciprofloxacin resistance in methicillin-resistant Staphylococcus aureus: analysis by polymerase chain reaction and automated direct DNA sequencing

A portion of the gyrA gene from amino acid codons 67 to 129 was sequenced in 34 methicillin-resistant Staphylococcus aureus strains (14 isolated in Minnesota, 10 isolated in Indiana, and 10 isolated in Tennessee). Twenty-eight of these strains were ciprofloxacin resistant. Sixteen of the strains contained a Ser----Leu mutation at codon 84; 3 contained strains a Ser----Ala mutation at codon 84; 3 strains contained two mutations, Ser----Leu at codon 84 and Ser----Pro at codon 85; and 6 strains contained a Glu----Lys mutation at codon 88. Six strains were wild type and ciprofloxacin susceptible. Several mutations from amino acid codons 84 through 88 can be associated with high-level quinolone resistance.
Step selection techniques uncover the environmental predictors of space use patterns in flocks of Amazonian birds

Understanding the behavioral decisions behind animal movement and space use patterns is a key challenge for behavioral ecology. Tools to quantify these patterns from movement and animal–habitat interactions are vital for transforming ecology into a predictive science. This is particularly important in environments undergoing rapid anthropogenic changes, such as the Amazon rainforest, where animals face novel landscapes. Insectivorous bird flocks are key elements of avian biodiversity in the Amazonian ecosystem. Therefore, disentangling and quantifying the drivers behind their movement and space use patterns is of great importance for Amazonian conservation. We use a step selection function (SSF) approach to uncover environmental drivers behind movement choices. This is used to construct a mechanistic model, from which we derive predicted utilization distributions (home ranges) of flocks. We show that movement decisions are significantly influenced by canopy height and topography, but depletion and renewal of resources do not appear to affect movement significantly. We quantify the magnitude of these effects and demonstrate that they are helpful for understanding various heterogeneous aspects of space use. We compare our results to recent analytic derivations of space use, demonstrating that the analytic approximation is only accurate when assuming that there is no persistence in the animals' movement. Our model can be translated into other environments or hypothetical scenarios, such as those given by proposed future anthropogenic actions, to make predictions of spatial patterns in bird flocks. Furthermore, our approach is quite general, so could potentially be used to understand the drivers of movement and spatial patterns for a wide variety of animal communities.
Dominant Role of Paraoxonases in Inactivation of the Pseudomonas aeruginosa Quorum-Sensing Signal N-(3-Oxododecanoyl)-l-Homoserine Lactone

ABSTRACT The pathogenic bacterium Pseudomonas aeruginosa causes serious infections in immunocompromised patients. N-(3-Oxododecanoyl)-l-homoserine lactone (3OC12-HSL) is a key component of P. aeruginosa's quorum-sensing system and regulates the expression of many virulence factors. 3OC12-HSL was previously shown to be hydrolytically inactivated by the paraoxonase (PON) family of calcium-dependent esterases, consisting of PON1, PON2, and PON3. Here we determined the specific activities of purified human PONs for 3OC12-HSL hydrolysis, including the common PON1 polymorphic forms, and found they were in the following order: PON2 ≫ PON1192R > PON1192Q > PON3. PON2 exhibited a high specific activity of 7.6 ± 0.4 μmols/min/mg at 10 μM 3OC12-HSL, making it the best PON2 substrate identified to date. By use of class-specific inhibitors, approximately 85 and 95% of the 3OC12-HSL lactonase activity were attributable to PON1 in mouse and human sera, respectively. In mouse liver homogenates, the activity was metal dependent, with magnesium- and manganese-dependent lactonase activities comprising 10 to 15% of the calcium-dependent activity. In mouse lung homogenates, all of the activity was calcium dependent. The calcium-dependent activities were irreversibly inhibited by extended EDTA treatment, implicating PONs as the major enzymes inactivating 3OC12-HSL. In human HepG2 and EA.hy 926 cell lysates, the 3OC12-HSL lactonase activity closely paralleled the PON2 protein levels after PON2 knockdown by small interfering RNA treatment of the cells. These findings suggest that PONs, particularly PON2, could be an important mechanism by which 3OC12-HSL is inactivated in mammals.
Cross-Layer Design for Energy-Efficient Reliable Routing in Wireless Sensor Networks

Delivering sensed data to the sink reliably in wireless sensor networks (WSN) calls for a Delivering sensed data to the sink reliably in wireless sensor networks (WSN) calls for a scalable, energy-efficient, and error-resilient routing solution. In this paper, a distributed energy-efficient and reliable routing protocol is proposed using cross-layer design techniques, by jointly considering the routing algorithm in network layer and the power control policy in physical layer. Based on the analysis of how to construct a minimum-power route with the end-to-end reliability constraint in WSN, a distributed cross-layer routing protocol with adaptive transmission power control (DRPC) is proposed. Evaluation results show that our strategy performs better than other routing algorithms in terms of energy efficiency as well as reliability.
Is Antioxidant and n–3 Supplementation Able to Improve Functional Status in Poststroke Patients? Results from the Nutristroke Trial

Background: To test whether supplementary antioxidants and n–3 fatty acids, alone or in combination, could improve functional status in stroke survivors. Methods: We performed a randomized, double-blind, placebo-controlled clinical trial in 72 stroke patients (47 males; age 65.3 ± 12.9 years) admitted to a rehabilitation hospital for sequelae of first-ever ischemic stroke, and divided them into 4 subgroups. Group 1 patients received daily oral antioxidants, group 2 received n–3 polyunsaturated fatty acids, group 3 both supplements, and group 4 placebo, all for 12 months. No difference at baseline was observed among groups in neurological severity or in disability. All measures were repeated after 6 and 12 months of treatment. All major clinical events were recorded. Results: At baseline, 25% of the patients had a low plasma vitamin status, and 48.5% was at risk of undernutrition. At the 1-year follow-up, we observed a trend for lower mortality (p = 0.060) in subgroups treated with n–3 fatty acids, but without significant differences in rehabilitation result status among groups. Conclusions: Malnutrition is widely observed in patients admitted to a rehabilitative hospital for stroke rehabilitation, and dietary supplementation, even if not able to improve rehabilitation results, is likely to reduce mortality at the 1-year follow-up.
Computational Phenotyping of Two-Person Interactions Reveals Differential Neural Response to Depth-of-Thought

Reciprocating exchange with other humans requires individuals to infer the intentions of their partners. Despite the importance of this ability in healthy cognition and its impact in disease, the dimensions employed and computations involved in such inferences are not clear. We used a computational theory-of-mind model to classify styles of interaction in 195 pairs of subjects playing a multi-round economic exchange game. This classification produces an estimate of a subject's depth-of-thought in the game (low, medium, high), a parameter that governs the richness of the models they build of their partner. Subjects in each category showed distinct neural correlates of learning signals associated with different depths-of-thought. The model also detected differences in depth-of-thought between two groups of healthy subjects: one playing patients with psychiatric disease and the other playing healthy controls. The neural response categories identified by this computational characterization of theory-of-mind may yield objective biomarkers useful in the identification and characterization of pathologies that perturb the capacity to model and interact with other humans.
Object detection via foreground contour feature selection and part-based shape model

In this paper, we propose a novel approach for object detection via foreground feature selection and part-based shape model. It automatically learns a shape model from cluttered training images without need to explicitly given bounding box on objects. Our approach commences by extracting a set of feature descriptors, and iteratively selects the foreground features using Earth Movers Distances based matching. This leads to a part-based shape model that can be used for object detection. Experimental results show that the proposed method has comparable performance with the state-of-the-art shape-based detection methods but with less requirements on the data at the training stage.
Effects of Self-Rated Health and Self-Rated Economic Situation on Depressed Mood Via Life Satisfaction Among Older Adults in Costa Rica

Objective: The study examined the relationship of self-rated health and self-rated economic situation with depressed mood, and life satisfaction as mediator of this relationship among older adults in Costa Rica. Method: A longitudinal study was conducted with a subsample (N = 1,618) from the Costa Rican Longevity and Healthy Aging Study (CRELES). Self-rated health, self-rated economic situation, depressed mood, and life satisfaction were measured at baseline, and depressed mood was reassessed 18 months later. Putative mechanisms for changes in depressed mood were examined by means of conditional process analysis. Results: Self-rated health was negatively associated to depressed mood. This effect took place via life satisfaction. An interaction showed that better economic situation compensated the effect of a low self-rated health on life satisfaction. Discussion: This study suggests that subjective variables such as self-rated health, economic situation, and life satisfaction should be considered when addressing the onset of depressed mood.
Navigational Style Influences Eye Movement Pattern during Exploration and Learning of an Environmental Map

During navigation people may adopt three different spatial styles (i.e., Landmark, Route, and Survey). Landmark style (LS) people are able to recall familiar landmarks but cannot combine them with directional information; Route style (RS) people connect landmarks to each other using egocentric information about direction; Survey style (SS) people use a map-like representation of the environment. SS individuals generally navigate better than LS and RS people. Fifty-one college students (20 LS; 17 RS, and 14 SS) took part in the experiment. The spatial cognitive style (SCS) was assessed by means of the SCS test; participants then had to learn a schematic map of a city, and after 5 min had to recall the path depicted on it. During the learning and delayed recall phases, eye-movements were recorded. Our intent was to investigate whether there is a peculiar way to explore an environmental map related to the individual’s spatial style. Results support the presence of differences in the strategy used by the three spatial styles for learning the path and its delayed recall. Specifically, LS individuals produced a greater number of fixations of short duration, while the opposite eye movement pattern characterized SS individuals. Moreover, SS individuals showed a more spread and comprehensive explorative pattern of the map, while LS individuals focused their exploration on the path and related targets. RS individuals showed a pattern of exploration at a level of proficiency between LS and SS individuals. We discuss the clinical and anatomical implications of our data.
Two-pass MPEG-2 variable-bit-rate encoding

Many MPEG-2 encoding applications are real-time; this implies that the video signal must be encoded with no significant lookahead. However, there exist non-real-time applications that do enable us to first analyze a video sequence entirely, and, using the analysis results, to optimize a second encoding pass of the same data. One example of such an application is the digital video disk (DVD), which is designed to facilitate a variable-bit-rate (VBR) output stream. In that case, it is possible to let the MPEG-2 encoder produce a video sequence with a constant visual quality over time. This is in contrast to constant-bit-rate (CBR) systems, where the rate is constant but the visual quality varies with the coding difficulty. This paper describes a two-pass encoding system that has as its objective to produce an optimized VBR data stream in a second pass. In a first pass, the video sequence is encoded with CBR, while statistics concerning coding complexity are gathered. Next, the first-pass data is processed to prepare the control parameters for the second pass, which performs the actual VBR compression. In this off-line processing stage, we determine the target number of bits for each picture in the sequence, such that we realize the VBR objective. This means that the available bits are appropriately distributed over the different video segments such that constant visual quality is obtained. To be able to quantify the constant visual quality, perceptual experiments are described and a practical model is fitted to them. Exceptional cases such as scene changes and fades are detected and dealt with appropriately. We also ensure that the second-pass compression process does not violate the decoder buffer boundaries. Finally, the encoding is performed again, but now under control of the processed first-pass data. During the running of this second pass, a run-time bit-production control mechanism monitors the accuracy and validity of the first-pass data, correcting errors in prediction and observing the buffer boundaries. Results are compared to CBR operation.
Preparation of transfersomes encapsulating sildenafil aimed for transdermal drug delivery: Plackett–Burman design and characterization

Abstract The aim of this work was to study the effect of different processing and formulation parameters on the preparation of sildenafil (SD) transfersomes utilizing the Plackett–Burman design. The drug to phospholipid molar ratio (X1), phospholipid to surfactant ratio (X2), hydrophilic–lipophilic balance of the surfactant (X3), hydration medium pH (X4), hydration time (X5) and the temperature of hydration (X6) were investigated to study their effect on the vesicle size (Y1) and entrapment efficiency (EE) of the drug (Y2). The preparation conditions were optimized to minimize the vesicle size and maximize the EE. The prepared transfersomes were also subjected to zeta potential measurements, morphological and physicochemical characterization. The combinations of factors that achieve the optimum desirability were identified. An optimized formulation was prepared and characterized once more for its vesicle size, EE, in vitro permeation and deformability index. The results revealed that both X3 and X6 had a pronounced effect on Y1, while X1 and X4 showed a significant effect on Y2. Morphological and physicochemical study confirmed the transfersomes spherical shape and compatibility of the formulation ingredients. The formulation with optimum desirability showed EE and vesicle size of 97.21% and 610 nm, respectively. In vitro permeation of the drug-loaded transfersome showed more than 5-fold higher permeation rate compared with drug suspension. Deformability index verified elasticity of the preparation. The significant variables could be optimized again to produce smaller vesicle size that could increase SD permeation from transdermal delivery systems loaded drug optimized transfersomes.
Epidemiological aspects of centipede (Scolopendromorphae: Chilopoda) bites registered in greater S. Paulo, SP, Brazil.

INTRODUCTION The lack of basic knowledge on venomous arthropods and the benignity of the clinical manifestations contribute to the centipede bite victims' not being taken to a treatment reference center, leading to underestimation of the number of cases and minimizing the possibility of a broader epidemiological view. An inventory of the centipede bite occurrences in Greater S. Paulo, Brazil, and the therapeutic methods employed, by the main Brazilian medical center for the notification of poisoning by venomous animals, is presented. METHOD All patient cards of the period 1980-1989 have been checked as to place, month and time of occurrence; sex, age, affected part of the body, signs and symptoms have been observed, as well as the therapeutic methods employed. The centipedes that caused the accidents were identified at the Arthropods Laboratory. RESULTS It was registered 216 accidents, with a 69% predominance of the Greater S. Paulo and in only 63% of the cases (136) was the agent brought in by the victim for identification. The genera most frequently represented were Cryptops (58%), Otostigmus (33%) and Scolopendra (4%). Of the 136 cases, 87% showed erythema, edema, hemorrhage, burns, cephalalgia, and intense pain. There was a predominance of accidents in the warm rainy season, in the morning and for females between 21 and 60 years of age. Hands and feet were the parts of the body most affected. The benign evolution of the clinical picture (54%) made therapeutical treatment unnecessary. Only the victims of Scolopendra and Otostigmus (46%) were medicated with anesthetics (51%), analgesics (25%), antihistamines and cortisone (24%). CONCLUSION The reproductive period of the centipedes, associated with their sinanthropic habits, contributes to the greater incidence of accidents in urban areas in the warm rainy season. Only patients bitten by Scolopendra and Otostigmus require therapeutical treatment.
Influence of Combined Afferent Stimulation and Task-Specific Training Following Stroke: A Pilot Randomized Controlled Trial

Background. Reorganization of the human motor cortex can be induced by specific patterns of peripheral afferent stimulation. The potential for afferent stimulation to facilitate the functional recovery associated with conventional rehabilitative techniques has not previously been investigated. Objective. The authors sought to determine whether combining appropriate afferent stimulation with task-specific training resulted in greater improvements than training alone in patients with impaired upper limb function in the subacute phase following stroke. Method. Twenty patients with hemiparesis due to stroke were allocated randomly to either a stimulation or control group. All received 9 sessions of task-specific physiotherapy training over 3 weeks. Prior to each training session, associative electrical stimulation of the motor point of 2 hand muscles was given in the stimulation group, whereas the control group received sham stimulation. Changes in dexterity were assessed using a grip-lift task, and standard measures of upper-limb function were made before and following the intervention. Corticospinal excitability was examined using transcranial magnetic stimulation. Results. Both groups showed comparable improvements in functional measures of upper-limb function. Of the 20 patients, only 14 could perform the grip-lift task, which is an objective measure of dexterity. Patients in the stimulation group From the Research Centre for Human Movement Control, School of exhibited significantly greater improvements in this task than the control group. There was no significant change in corticospinal excitability in either group. Conclusion. This pilot study provides preliminary data suggesting that targeted afferent stimulation may facilitate the response to conventional rehabilitation in patients with hemiparesis due to stroke, but these results need to be confirmed in a larger scale study.
Detection and Molecular Characterization of Calf Diarrhoea Bovine Coronaviruses Circulating in South Korea during 2004–2005

Although the widespread occurrence of calf diarrhoea (CD) bovine coronavirus (BCoV) infections have been reported in most cattle producing countries, only the genetic differences in the BCoVs from American and Canadian isolates and/or strains have been identified and compared. Hence, it is unclear if the BCoVs circulating in the other countries have distinct genetic characteristics. The aim of this study was to determine the prevalence and genetic diversity of CD BCoVs based on the deduced amino acid (aa) sequences of the spike (S) and haemagglutinin/esterase (HE) proteins in South Korea. RT‐PCR and nested PCR using the primer pairs specific to the nucleocapsid gene, BCoVs detected the BCoVs in 56 (15.6%) of 359 diarrhoeic faecal samples. Phylogenetic analysis of the entire S gene indicated that 10 Korean CD BCoV strains clustered with other Korean BCoV strains with different clinical forms but were different from the American and Canadian BCoV strains. Moreover, the phylogenetic data of the aa sequences of the HE gene revealed all the Korean CD strains to be distinct from the other Korean BCoV strains with different clinical forms. These results suggest that the Korean BCoVs cause endemic infections in diarrhoeic calves in Jeonnam province and have taken a different evolutionary pathway from the BCoVs in other countries. Moreover, the different BCoV strains are circulating in the different clinical forms in South Korea. These results also suggest that vaccines against the BCoVs can be developed with each Korean BCoV in different clinical forms.
Blockade of monoacylglycerol lipase inhibits oligodendrocyte excitotoxicity and prevents demyelination in vivo

The endocannabinoids 2‐araquidonoylglycerol (2‐AG) and anandamide (AEA) are bioactive lipids crucially involved in the regulation of brain function in basal and pathological conditions. Blockade of endocannabinoid metabolism has emerged as a promising therapeutic strategy for inflammatory diseases of the central nervous system, including myelin disorders such as multiple sclerosis. Nevertheless, the biological actions of endocannabinoid degradation inhibitors in oligodendrocytes and white matter tracts are still ill defined. Here we show that the selective monoacylglycerol lipase (MAGL) inhibitor JZL184 suppressed cell death by mild activation of AMPA receptors in oligodendrocytes in vitro, an effect that was mimicked by MAGL substrate 2‐AG and by the second major endocannabinoid AEA, in a concentration‐dependent manner, whereas inhibition of the AEA metabolizing enzyme fatty acid amide hydrolase with URB597 was devoid of effect. Pharmacological experiments suggested that oligodendrocyte protection from excitotoxicity resulting from MAGL blockade involved the activation of cannabinoid CB1 receptors and the reduction of AMPA‐induced cytosolic calcium overload, mitochondrial membrane depolarization, and production of reactive oxygen species. Administration of JZL184 under a therapeutic regimen decreased clinical severity, prevented demyelination, and reduced inflammation in chronic experimental autoimmune encephalomyelitis. Furthermore, MAGL inactivation robustly preserved myelin integrity and suppressed microglial activation in the cuprizone‐induced model of T‐cell‐independent demyelination. These findings suggest that MAGL blockade may be a useful strategy for the treatment of immune‐dependent and ‐independent damage to the white matter. GLIA 2015;63:163–176