Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas aeruginosa Biofilm Antibiotic Resistance Gene ndvB Expression Requires the RpoS Stationary-Phase Sigma Factor

ABSTRACT Chronic, biofilm-based bacterial infections are exceptionally difficult to eradicate due to the high degree of antibiotic recalcitrance exhibited by cells in biofilm communities. In the opportunistic pathogen Pseudomonas aeruginosa, biofilm recalcitrance is multifactorial and arises in part from the preferential expression of resistance genes in biofilms compared to exponential-phase planktonic cells. One such mechanism involves ndvB, which we have previously shown to be expressed specifically in biofilms. In this study, we investigated the regulatory basis of this lifestyle-specific expression by developing an unstable green fluorescent protein (GFP) transcriptional reporter to observe the expression pattern of ndvB. We found that in addition to its expression in biofilms, ndvB was upregulated in planktonic cells as they enter stationary phase. The transcription of ndvB in both growth phases was shown to be dependent on the stationary-phase sigma factor RpoS, and mutation of a putative RpoS binding site in the ndvB promoter abolished the activity of the promoter in stationary-phase cells. Overall, we have expanded our understanding of the temporal expression of ndvB in P. aeruginosa and have uncovered a regulatory basis for its growth phase-dependent expression. IMPORTANCE Bacterial biofilms are more resistant to antibiotics than free-living planktonic cells, and understanding the mechanistic basis of this resistance can inform treatments of biofilm-based infections. In addition to chemical and structural barriers that can inhibit antibiotic entry, the upregulation of specific genes in biofilms contributes to the resistance. We investigated this biofilm-specific gene induction by examining expression patterns of ndvB, a gene involved in biofilm resistance of the opportunistic pathogen Pseudomonas aeruginosa. We characterized ndvB expression in planktonic and biofilm growth conditions with an unstable green fluorescent protein (GFP) reporter and found that the expression of ndvB in biofilms is dependent on the stationary-phase sigma factor RpoS. Overall, our results support the physiological similarity between biofilms and stationary-phase cells and suggest that the induction of some stationary-phase genes in biofilms may contribute to their increased antibiotic resistance.
Dissociated Components of Executive Control in Acute Hypobaric Hypoxia.

INTRODUCTION The neurocognitive effects of acute hypobaric hypoxia are still largely unknown. This study was designed to test the hypothesis that executive control, an important component of cognition, is especially vulnerable to hypoxia. METHODS Subjects participated in a simulated hypobaric chamber flight to 5500 m. Four auditory tasks were presented before, during, and after hypoxia: 1) Voice, and 2) Name variant of the Stroop task (both measuring conflict resolution); 3) go/no-go task (GNG; measuring inhibition); and 4) two-choice reaction time task (CRT; which is a noninhibitory control task). RESULTS The Stroop effect increased during hypoxia: in the Voice Stroop it increased from 49.4 to 83.6 ms for reaction time and from 4.1 to 12.3% for accuracy; in the Name Stroop from 43.5 to 82.9 ms for reaction time (accuracy remained unchanged). Accuracy declined from 82.3 to 75.0% in CRT, and from 85.8 to 77.5% (averaged over stimulus types) in the GNG task. Importantly, accuracy decreased similarly to go and no-go stimuli in the GNG task, revealing unaffected inhibition. DISCUSSION The findings suggest that tasks requiring conflict resolution are more likely to be impaired than tasks requiring inhibition of response. Furthermore, our results provide evidence for the distinct nature of inhibitory control functions. Takács E, Czigler I, Pató LG, Balázs L. Dissociated components of executive control in acute hypobaric hypoxia. Aerosp Med Hu Perform. 2017; 88(12):1081-1087.
A Unifying Framework of Synaptic and Intrinsic Plasticity in Neural Populations

A neuronal population is a computational unit that receives a multivariate, time-varying input signal and creates a related multivariate output. These neural signals are modeled as stochastic processes that transmit information in real time, subject to stochastic noise. In a stationary environment, where the input signals can be characterized by constant statistical properties, the systematic relationship between its input and output processes determines the computation carried out by a population. When these statistical characteristics unexpectedly change, the population needs to adapt to its new environment if it is to maintain stable operation. Based on the general concept of homeostatic plasticity, we propose a simple compositional model of adaptive networks that achieve invariance with regard to undesired changes in the statistical properties of their input signals and maintain outputs with well-defined joint statistics. To achieve such invariance, the network model combines two functionally distinct types of plasticity. An abstract stochastic process neuron model implements a generalized form of intrinsic plasticity that adapts marginal statistics, relying only on mechanisms locally confined within each neuron and operating continuously in time, while a simple form of Hebbian synaptic plasticity operates on synaptic connections, thus shaping the interrelation between neurons as captured by a copula function. The combined effect of both mechanisms allows a neuron population to discover invariant representations of its inputs that remain stable under a wide range of transformations (e.g., shifting, scaling and (affine linear) mixing). The probabilistic model of homeostatic adaptation on a population level as presented here allows us to isolate and study the individual and the interaction dynamics of both mechanisms of plasticity and could guide the future search for computationally beneficial types of adaptation.
Learning Visual Features from Snapshots for Web Search

When applying learning to rank algorithms to Web search, a large number of features are usually designed to capture the relevance signals. Most of these features are computed based on the extracted textual elements, link analysis, and user logs. However, Web pages are not solely linked texts, but have structured layout organizing a large variety of elements in different styles. Such layout itself can convey useful visual information, indicating the relevance of a Web page. For example, the query-independent layout (i.e., raw page layout) can help identify the page quality, while the query-dependent layout (i.e., page rendered with matched query words) can further tell rich structural information (e.g., size, position and proximity) of the matching signals. However, such visual information of layout has been seldom utilized in Web search in the past. In this work, we propose to learn rich visual features automatically from the layout of Web pages (i.e., Web page snapshots) for relevance ranking. Both query-independent and query-dependent snapshots are considered as the new inputs. We then propose a novel visual perception model inspired by human's visual search behaviors on page viewing to extract the visual features. This model can be learned end-to-end together with traditional human-crafted features. We also show that such visual features can be efficiently acquired in the online setting with an extended inverted indexing scheme. Experiments on benchmark collections demonstrate that learning visual features from Web page snapshots can significantly improve the performance of relevance ranking in ad-hoc Web retrieval tasks.
New Results for Wireless Multihop Diversity Systems

We study the performance of multihop diversity systems with non-regenerative relays over independent and non-identical Rayleigh fading channels. The analysis is based on the evaluation of the instantaneous end-to-end signal-to-noise ratio (SNR), depending on the type of the relay and the diversity scheme used. A closed-form expression is derived for the average end-to-end SNR, when fixed-gain relays and a maximal ratio combiner (MRC) are used, whereas an analytical expression formula for the average symbol-error rate, is presented. The results show that multihop diversity systems outperform conventional telecommunication systems in terms of ASER when the same amount of energy is assumed to be consumed in both cases.
Fracture mechanism of ferritic ductile cast iron in extremely low cycle fatigue

Low cycle fatigue tests were carried out under push-pull loading conditions using Ferritic Ductile Cast Iron (FDI). In order to clarify the fatigue fracture mechanism of FDI in an Extremely Low Cycle Fatigue (ELCF) regime, an observation of the longitudinal sections of the partially fatigued specimens were performed. The fatigue process in the ELCF regime can be classified into three stages : (a) Generation of micro voids, caused by the debonding of the graphite-matrix interface. (b) Growth of the micro voids, perpendicular to the loading axis. (c) Formation of an internal macro crack, due to the coalescence of micro voids inside the material. Two types of microvoid coalescence processes have been observed. The first, due to the growth of internal micro-cracks and the second, due to internal necking of the matrix. The fatigue process of the FDI in the ELCF regime was accompained by the static fracture mechanism.
Clb6-Cdc28 Promotes Ribonucleotide Reductase Subcellular Redistribution during S Phase

ABSTRACT A tightly controlled cellular deoxyribonucleotide (deoxynucleoside triphosphate [dNTP]) pool is critical for maintenance of genome integrity. One mode of dNTP pool regulation is through subcellular localization of ribonucleotide reductase (RNR), the enzyme that catalyzes the rate-limiting step of dNTP biosynthesis. In Saccharomyces cerevisiae, the RNR small subunit, Rnr2-Rnr4, is localized to the nucleus, whereas the large subunit, Rnr1, is cytoplasmic. As cells enter S phase or encounter DNA damage, Rnr2-Rnr4 relocalizes to the cytoplasm to form an active holoenzyme complex with Rnr1. Although the DNA damage-induced relocalization requires the checkpoint kinases Mec1-Rad53-Dun1, the S-phase-specific redistribution does not. Here, we report that the S-phase cyclin–cyclin-dependent kinase (CDK) complex Clb6-Cdc28 controls Rnr2-Rnr4 relocalization in S phase. Rnr2 contains a consensus CDK site and exhibits Clb6-dependent phosphorylation in S phase. Deletion of CLB6 or removal of the CDK site results in an increased association of Rnr2 with its nuclear anchor Wtm1, nuclear retention of Rnr2-Rnr4, and an enhanced sensitivity to the RNR inhibitor hydroxyurea. Thus, we propose that Rnr2-Rnr4 redistribution in S phase is triggered by Clb6-Cdc28-mediated phosphorylation of Rnr2, which disrupts the Rnr2-Wtm1 interaction and promotes the release of Rnr2-Rnr4 from the nucleus.
An IP Protection Algorithm by Watermarking Multiple Scan Chains Based on Minimum Correlation Degree of Vectors

With the rapid development of deep sub-micron integrated circuit systems, existing Intellectual Property (IP) watermarking methods for scan chains are mainly implemented by reordering and reconstructing scan chain for protecting reused IP cores. These methods may cause high vector correlation of IP watermark, which will seriously affect overhead and reliability. A multiple scan chains-based IP protection method with minimum test vectors was proposed in this paper. Firstly, the test vector sequence for scan input was generated by the generator of pseudo-random test vector, then the multiple scan chains-based watermarking structure with minimum correlation degree of vectors were constructed by combining the generated sequence with the circuit-under-test. By adding constraints in the structure, watermark would be restricted to positions of certain scan cells. Finally, the watermark was inserted and extracted by altering states of specific registers in scan cells with the designed logic circuit for bit alteration. With no influence on normal circuit function, the proposed algorithm could embed and extract the information of the user's legitimate ownership and effectively address high power overhead and low security. The experiments were conducted on ISCAS-89 benchmarks. The results showed that the resource overhead in watermark embedding was reduced by more than 8% under the condition of adding constraints.
Renal and Hematologic Comparative Effects of Dissociated Agonist of the Glucocorticoid Receptor and Prednisone in Dogs With and Without Food Restriction

Glomerulopathy and body weight gain were noted after chronic oral administration of a novel nonsteroidal dissociated agonist of the glucocorticoid receptor compound, fosdagrocorat, to beagle dogs fed an ad libitum diet. To further investigate the role of diet and treatment with either fosdagrocorat or the glucocorticoid comparator, prednisone, on renal safety, a 13-week investigative study was conducted in beagle dogs. Renal histopathology, clinical chemistry, urinalysis, glomerular filtration rate (GFR), body weight, heart rate, blood pressure (BP), and hematology were investigated in restricted- and ad libitum-fed dogs administered prednisone (2.2 mg/kg/d), fosdagrocorat (5 mg/kg/d), or vehicle for 13 weeks. Glomerulopathy was primarily observed in fosdagrocorat- and prednisone-treated ad libitum but not in feed-restricted or ad libitum vehicle-treated dogs. Kidneys in dogs from the prednisone-treated ad libitum had the greatest incidence and severity of tubular degenerative changes. Increased urine volume and decreased urine-specific gravity were present in prednisone- and fosdagrocorat-treated dogs, regardless of diet. These changes were not associated with consistent changes in GFR. Fosdagrocorat or prednisone treatment ad libitum dogs had the greatest increase in body weight gain. Sporadic changes in systolic and diastolic BP were noted in fosdagrocorat- and prednisone-treated groups. Significant reductions in serum cortisol and absolute eosinophils were noted in both ad libitum- and restriction-fed prednisone- and fosdagrocorat-treated dogs. In conclusion, prednisone-treated dogs fed ad libitum had greater glucocorticoid-induced renal effects than those dosed with fosdagrocorat.
UVB promotes the initiation of uveitic inflammatory injury in vivo and is attenuated by UV-blocking protection

Purpose Uveitic inflammatory injury can cause irreversible visual loss; however, no single animal model recapitulates all the characteristics of human uveitis. Ultraviolet radiation (UVR) is one of the risk factors for uveitis, but the role of UVR in the pathogenesis of uveitic injury is unclear. The aim of this study was to elucidate whether UVB promotes the initiation of, and subsequently contributes to, uveitic inflammatory injury. Methods Mice were assigned to either a blank control group or one of three UVB treatment groups: no protection, protection with Nelfilcon A contact lens (Food and Drug Administration [FDA] class II, about 46.8% UVB transmittance), or protection with Etafilcon A contact lens (FDA class IV, about 0.55% UVB transmittance). The contact lenses acted as blocking barriers against UVR. After the application of UVR, pathologic injuries were determined with slit-lamp microscopy and histologic examination. Results Compared with the intact status of the controls, the anterior eyes of the UVB groups showed pathologic alterations in physiologic properties and tissue integrity. UVR promoted anterior uveitic inflammatory injury, with expansion of the hyperemic iris vessels, over-production of aqueous humor protein, disruption of the blood–aqueous barrier, and embedding of infiltrative leukocytes inside the iridocorneal angle. However, blockage of UVR in vivo retarded the progression of uveitic inflammatory injury. The highest level of UV protection in the Etafilcon A group resulted in greater inhibition of uveitic inflammatory injury than that in the Nelfilcon A group. Conclusions This study demonstrates that UVB initiated and promoted uveitic inflammatory injury. UV protection is needed for the clinical management of anterior uveitis. The Etafilcon A lenses provide better protection of the anterior segment of the eye against UVB damage compared with the Nelfilcon A lenses.
Targeting experimental orthotopic glioblastoma with chitosan-based superparamagnetic iron oxide nanoparticles (CS-DX-SPIONs)

Background Glioblastoma is the most devastating primary brain tumor of the central nervous system in adults. Magnetic nanocarriers may help not only for a targeted delivery of chemotherapeutic agents into the tumor site but also provide contrast enhancing properties for diagnostics using magnetic resonance imaging (MRI). Methods Synthesized hybrid chitosan-dextran superparamagnetic nanoparticles (CS-DX-SPIONs) were characterized using transmission electron microscopy (TEM) and relaxometry studies. Nonlinear magnetic response measurements were employed for confirming the superparamagnetic state of particles. Following in vitro analysis of nanoparticles cellular uptake tumor targeting was assessed in the model of the orthotopic glioma in rodents. Results CS-DX-SPIONs nanoparticles showed a uniform diameter of 55 nm under TEM and superparamagentic characteristics as determined by T1 (spin-lattice relaxation time) and T2 (spin-spin relaxation time) proton relaxation times. Application of the chitosan increased the charge from +8.9 to +19.3 mV of the dextran-based SPIONs. The nonlinear magnetic response at second harmonic of CS-DX-SPIONs following the slow change of stationary magnetic fields with very low hysteresis evidenced superparamagnetic state of particles at ambient temperatures. Confocal microscopy and flow cytometry studies showed an enhanced internalization of the chitosan-based nanoparticles in U87, C6 glioma and HeLa cells as compared to dextran-coated particles. Cytotoxicity assay demonstrated acceptable toxicity profile of the synthesized nanoparticles up to a concentration of 10 μg/ml. Intravenously administered CS-DX-SPIONs in orthotopic C6 gliomas in rats accumulated in the tumor site as shown by high-resolution MRI (11.0 T). Retention of nanoparticles resulted in a significant contrast enhancement of the tumor image that was accompanied with a dramatic drop in T2 values (P<0.001). Subsequent histological studies proved the accumulation of the nanoparticles inside glioblastoma cells. Conclusion Hybrid chitosan-dextran magnetic particles demonstrated high MR contrast enhancing properties for the delineation of the brain tumor. Due to a significant retention of the particles in the tumor an application of the CS-DX-SPIONs could not only improve the tumor imaging but also could allow a targeted delivery of chemotherapeutic agents.
Low-birth-weight, but not catch-up growth, correlates with insulin resistance and resistin level in SGA infants at 12 months

Abstract Objective: To investigate the insulin resistance status in SGA infants at 12 months and its relationship with auxological and metabolic parameters. Methods: One group of 45 SGA and one of 50 appropriate for gestational age infants were followed from birth to the end of the first year of life. At 12 months, skinfold thickness, waist circumference, and blood levels of glucose, insulin, adiponectin, leptin, resistin, visfatin, retinol-binding protein 4, IGFs, lipids profile were determined, and the HOMA-IR index was calculated. Results: The SGAs had increased insulin (5.2 ± 2.7 versus 2.9 ± 2.4 μIU/ml, p = 0.012) and HOMA-IR (1.09 ± 0.9 versus 0.59 ± 0.55, p = 0.016). In multiple regression, insulin resistance indices were independently correlated with low-birth-weight (β = −2.92, p = 0.015 for insulin, β = −2.98, p = 0.011 for HOMA-IR) but not with catch-up growth in either height or weight or any other metabolic parameter. Resistin was higher in the SGAs (5.1 ± 2.1 versus 3.9 ± 2.1 ng/ml, p = 0.03) and independently correlated with low-birth-weight but not insulin resistance. Resistin was negatively correlated with total cholesterol (R = −0.33, p = 0.007) and positively with lipoprotein(a) (R = 0.49, p = 0.001). Conclusion: Low-birth-weight, but not catch-up growth or adiposity tissue hormones, was correlated with insulin resistance at 12 months in non-obese SGA infants. The higher resistin in SGA infants and its correlation with total cholesterol and lipoprotein(a) need further clarification.
Clinical assessment of the male fertility

The evaluation of infertility in males consists of physical examination and semen analyses. Standardized semen analyses depend on the descriptive analysis of sperm motility, morphology, and concentration, with a threshold level that must be surpassed to be considered a fertile spermatozoon. Nonetheless, these conventional parameters are not satisfactory for clinicians since 25% of infertility cases worldwide remain unexplained. Therefore, newer tests methods have been established to investigate sperm physiology and functions by monitoring characteristics such as motility, capacitation, the acrosome reaction, reactive oxygen species, sperm DNA damage, chromatin structure, zona pellucida binding, and sperm-oocyte fusion. After the introduction of intracytoplasmic sperm injection technique, sperm maturity, morphology, and aneuploidy conditions have gotten more attention for investigating unexplained male infertility. In the present article, recent advancements in research regarding the utilization of male fertility prediction tests and their role and accuracy are reviewed.
In Vitro Evaluation of Biofilm Dispersal as a Therapeutic Strategy To Restore Antimicrobial Efficacy

ABSTRACT As a proof-of-concept study, the direct impact of biofilm dispersal on the in vitro efficacy of imipenem and tobramycin was evaluated against 3-day-old biofilms of Pseudomonas aeruginosa. Arabinose induction of biofilm dispersal via activation of the phosphodiesterase YhjH in the P. aeruginosa engineered strain PAO1/pBAD-yhjH resulted in increased antimicrobial efficacy and synergy of the imipenem-tobramycin combination. These results support the use of biofilm dispersal to enhance antimicrobial efficacy in the treatment of biofilm-associated infections, representing a promising therapeutic strategy.
Eye Movements and Cognitive Strategy in a Fluid Intelligence Test: Item Type Analysis

Eye movements help to infer the cognitive strategy that a person uses in fluid intelligence tests. However, intelligence tests demand different relations/rules tokens to be solved, such as rule direction, which is the continuation, variation or overlay of geometric figures in the matrix of the intelligence test. The aim of this study was to understand whether eye movements could predict the outcome of an intelligence test and in the rule item groups. Furthermore, we sought to identify which measure is best for predicting intelligence test scores and to understand if the rule item groups use the same strategy. Accordingly, 34 adults completed a computerized intelligence test with an eye-tracking device. The toggling rate, that is, the number of toggles on each test item equalized by the item latency explained 45% of the variance of the test scores and a significant amount of the rule tokens item groups. The regression analyses also indicated toggling rate as the best measure for predicting the score and that all the rule tokens seem to respect the same strategy. No correlation or difference were found between baseline pupil size and fluid intelligence. Wiener Matrizen-Test 2 was demonstrated to be a good instrument for the purpose of this study. Finally, the implications of these findings for an understanding of cognition are discussed.