Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Virus–Host Cell Membrane Interaction: Membrane Voltage–Dependent Endocytic-like Entry of Bacteriophage φ6 Nucleocapsid

Studies on the virus-cell interactions have proven valuable in elucidating vital cellular processes. Interestingly, certain virus-host membrane interac- tions found in eukaryotic systems seem also to operate in prokaryotes (Bamford, D.H., M. Romantschuk, and P.J. Somerharju, 1987. EMBO (Eur. Mol. Biol. Organ.) J. 6:1467-1473; Romantschuk, M. , V.M. Olkkonen, and D.H. Bamford. 1988. EMBO (Eur. Mol. Biol. Organ.) J. 7:1821-1829). f 6 is an enveloped double-stranded RNA virus infecting a gram-negative bacterium. The vi- ral entry is initiated by fusion between the virus mem- brane and host outer membrane, followed by delivery of the viral nucleocapsid (RNA polymerase complex covered with a protein shell) into the host cytosol via an endocytic-like route. In this study, we analyze the inter- action of the nucleocapsid with the host plasma mem- brane and demonstrate a novel approach for dissecting the early events of the nucleocapsid entry process. The initial binding of the nucleocapsid to the plasma mem- brane is independent of membrane voltage ( DC ) and the K 1 and H 1 gradients. However, the following inter- nalization is dependent on plasma membrane voltage ( DC ), but does not require a high ATP level or K 1 and H 1 gradients. Moreover, the nucleocapsid shell protein, P8, is the viral component mediating the membrane- nucleocapsid interaction.
Expression of Cysteine Protease Cathepsin L is Increased in Endometrial Cancer and Correlates With Expression of Growth Regulatory Genes

Proteases contribute to tumor invasion and metastasis by degrading basement membranes and extracellular matrix (ECM). In this study, we compared gene expression levels of two proteases, cysteine protease Cathepsin L2 (CTSL2) and matrix metalloproteinase MMP11, in human endometrium and endometrial cancer. Our data demonstrate CTSL2 transcript levels to be strongly elevated in endometrial cancer, particularly in G3 tumors. Furthermore, we observed a highly significant positive correlation of CTSL2 with expression of growth regulatory genes Ki-67, cyclin B1, MYBL2, p21/WAF, and HER2 receptor tyrosine kinase. Our data suggest that CTSL2 might be involved in progression of endometrial cancer.
Noninvasive ventilation immediately after extubation improves lung function in morbidly obese patients with obstructive sleep apnea undergoing laparoscopic bariatric surgery.

BACKGROUND Noninvasive positive pressure ventilation (NIPPV) may improve postoperative lung function and reduce postoperative complications in patients undergoing abdominal surgery. The purpose of our study was to determine whether the timing of postoperative NIPPV affects lung function 1 day postoperatively. METHODS Forty morbidly obese patients with known obstructive sleep apnea undergoing laparoscopic bariatric surgery with standardized anesthesia care were randomly assigned to receive NIPPV immediately after tracheal extubation (immediate group) or supplemental oxygen (standard group). All patients had continuous positive airway pressure initiated 30 minutes after extubation in the postanesthesia care unit (PACU) via identical noninvasive ventilators. Spirometry was performed by a blinded observer in the perioperative holding area 1 hour after admission to the PACU and 1 day postoperatively. The primary outcome was the change in forced vital capacity (FVC) from baseline to 24 hours (FVC baseline-FVC 24 hours). RESULTS Forty patients, 20 in each group, were enrolled in the study. Forced expiratory volume in 1 second, FVC, and peak expiratory flow rate were significantly reduced in both groups from perioperative values throughout the study. At 24 hours, the intervention group had lost only 0.7 L FVC, versus 1.3 L for the intervention group (P = 0.0005). An analysis of covariance confirmed this and indicated that the immediate postoperative NIPPV better preserved spirometric function at 1 and 24 hours postoperatively. Specifically, the differences in the primary outcome were statistically significant. CONCLUSIONS NIPPV given immediately after extubation significantly improves spirometric lung function at 1 hour and 1 day postoperatively, compared with continuous positive airway pressure started in the PACU, in morbidly obese patients with obstructive sleep apnea undergoing laparoscopic bariatric surgery.
The galactose regulon of Escherichia coli

Galactose transport and metabolism in Escherichia coli involves a multicomponent amphibolic pathway. Galactose transport is accomplished by two different galactose‐specific transport systems. At least four of the genes and operons involved in galactose transport and metabolism have promoters containing similar regulatory sequences. These sequences are recognized by at least three regulators, Gal repressor (GalR), Gal isorepressor (GalS) and cAMP receptor protein (CRP), which modulate transcription from these promoters. The negative regulators, GalR and GalS, discriminate between utilization of the high‐affinity (regulated by GalS) and low‐affinity (regulated by GalR) transport systems, and modulate the expression of genes for galactose metabolism in an overlapping fashion. GalS is itself autogenously regulated and CRP dependent, while the gene for GalR is constitutive. The gal operon encoding the enzymes for galactose metabolism has two promoters regulated by CRP in opposite ways; one (P1) is stimulated and the other (P2) inhibited by CRP. Both promoters are strongly repressed by GalR but weakly by GalS. All but one of the constituent promoters of the gal regulon have two operators. The gal regulon has the potential to coordinate galactose metabolism and transport in a highly efficient manner, under a wide variety of conditions of galactose availability.
Interactive Rendering of Non‐Constant, Refractive Media Using the Ray Equations of Gradient‐Index Optics

Existing algorithms can efficiently render refractive objects of constant refractive index. For a medium with a continuously varying index of refraction, most algorithms use the ray equation of geometric optics to compute piecewise‐linear approximations of the non‐linear rays. By assuming a constant refractive index within each tracing step, these methods often need a large number of small steps to generate satisfactory images. In this paper, we present a new approach for tracing non‐constant, refractive media based on the ray equations of gradient‐index optics. We show that in a medium of constant index gradient, the ray equation has a closed‐form solution, and the intersection point between a ray and the medium boundaries can be efficiently computed using the bisection method. For general non‐constant media, we model the refractive index as a piecewise‐linear function and render the refraction by tracing the tetrahedron‐based representation of the media. Our algorithm can be easily combined with existing rendering algorithms such as photon mapping to generate complex refractive caustics at interactive frame rates. We also derive analytic ray formulations for tracing mirages – a special gradient‐index optical phenomenon.
Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns

SUMMARY Three recent publications have examined the quality and completeness of public database single nucleotide polymorphism (dbSNP) and have come to dramatically different conclusions regarding dbSNPs false positive rate and the proportion of dbSNPs that are expected to be common. These studies employed different genotyping technologies and different protocols in determining minimum acceptable genotyping quality thresholds. Because heterozygous sites typically have lower quality scores than homozygous sites, a higher minimum quality threshold reduces the number of false positive SNPs, but yields fewer heterozygotes and leads to fewer confirmed SNPs. To account for the different confirmation rates and distributions of minor allele frequencies, we propose that the three confirmation studies have different false positive and false negative rates. We developed a mathematical model to predict SNP confirmation rates and the apparent distribution of minor allele frequencies under user-specified false positive and false negative rates. We applied this model to the three published studies and to our own resequencing effort. We conclude that the dbSNP false positive rate is approximately 15-17% and that the reported confirmation studies have vastly different genotyping error rates and patterns.
Computational geometry for patient-specific reconstruction and meshing of blood vessels from MR and CT angiography

Investigation of three-dimensional (3-D) geometry and fluid-dynamics in human arteries is an important issue in vascular disease characterization and assessment. Thanks to recent advances in magnetic resonance (MR) and computed tomography (CT), it is now possible to address the problem of patient-specific modeling of blood vessels, in order to take into account interindividual anatomic variability of vasculature. Generation of models suitable for computational fluid dynamics is still commonly performed by semiautomatic procedures, in general based on operator-dependent tasks, which cannot be easily extended to a significant number of clinical cases. In this paper, we overcome these limitations making use of computational geometry techniques. In particular, 3-D modeling was carried out by means of 3-D level sets approach. Model editing was also implemented ensuring harmonic mean curvature vectors distribution on the surface, and model geometric analysis was performed with a novel approach, based on solving Eikonal equation on Voronoi diagram. This approach provides calculation of central paths, maximum inscribed sphere estimation and geometric characterization of the surface. Generation of adaptive-thickness boundary layer finite elements is finally presented. The use of the techniques presented here makes it possible to introduce patient-specific modeling of blood vessels at clinical level.
Analyzing Security Threats of Android-based Mobile Malware

Recently, mobile malware is rapidly growing due to increasing mobile service and device. In particular, mobile malware targeting Androidbased smartphones is growing because of open platform and market environments. In order to detect and response against mobile malware, mobile vaccines are widely used. However, the damages caused private data leak and financial charging have been reported frequently. In this paper, we have shown through experiments that it is possible to conduct DDoS attacks, private data leak, and illegal financial charging without detecting by mobile vaccine and have analyzed security vulnerabilities and threats in detail.
Interference-Constrained Pricing for D2D Networks

The concept of device-to-device (D2D) communications underlaying cellular networks opens up potential benefits for improving system performance but also brings new challenges, such as interference management. In this paper, we propose a pricing framework for interference management from the D2D users to the cellular system, where the base station (BS) protects itself (or its serving cellular users) by pricing the cross-tier interference caused from the D2D users. A Stackelberg game is formulated to model the interactions between the BS and D2D users. Specifically, the BS sets prices to maximize its revenue (or any desired utility) subject to an interference temperature constraint. For given prices, the D2D users competitively adapt their power allocation strategies for individual utility maximization. We first analyze the competition among the D2D users by noncooperative game theory and an iterative-based distributed power allocation algorithm is proposed. Then, depending on how much network information the BS knows, we develop two optimal algorithms, one for uniform pricing with limited network information and the other for differentiated pricing with global network information. The uniform pricing algorithm can be implemented by a fully distributed manner and requires minimum information exchange between the BS and D2D users, and the differentiated pricing algorithm is partially distributed and requires no iteration between the BS and D2D users. Then, a suboptimal differentiated pricing scheme is proposed to reduce complexity and it can be implemented in a fully distributed fashion. Extensive simulations are conducted to verify the proposed framework and algorithms.
Co-Evolving a Go-Playing Neural network

When evolving a game-playing neural network, fitness is usually measured by playing against existing opponents. In this article that need is overcome by applying the competitive coevolutionary techniques of competitive fitness sharing, shared sampling and hall of fame to the SANE neuro-evolution method. This approach is tested by evolving networks to play go on small boards. Networks evolved through co-evolution were compared against those evolved against the gnugo program. The co-evolutionary techniques were found to speed up the evolution and to result in better networks not limited by the quality of the opponent.
Computing Contingent Plans via Fully Observable Non-Deterministic Planning

Planning with sensing actions under partial observability is a computationally challenging problem that is fundamental to the realization of AI tasks in areas as diverse as robotics, game playing, and diagnostic problem solving. Recent work on generating plans for partially observable domains has advocated for online planning, claiming that offline plans are often too large to generate. Here we push the envelope on this challenging problem, proposing a technique for generating conditional (aka contingent) plans offline. The key to our planner's success is the reliance on state-of-the-art techniques for fully observable non-deterministic (FOND) planning. In particular, we use an existing compilation for converting a planning problem under partial observability and sensing to a FOND planning problem. With a modified FOND planner in hand, we are able to scale beyond previous techniques for generating conditional plans with solutions that are orders of magnitude smaller than previously possible in some domains.
A Complete Set of Nascent Transcription Rates for Yeast Genes

The amount of mRNA in a cell is the result of two opposite reactions: transcription and mRNA degradation. These reactions are governed by kinetics laws, and the most regulated step for many genes is the transcription rate. The transcription rate, which is assumed to be exercised mainly at the RNA polymerase recruitment level, can be calculated using the RNA polymerase densities determined either by run-on or immunoprecipitation using specific antibodies. The yeast Saccharomyces cerevisiae is the ideal model organism to generate a complete set of nascent transcription rates that will prove useful for many gene regulation studies. By combining genomic data from both the GRO (Genomic Run-on) and the RNA pol ChIP-on-chip methods we generated a new, more accurate nascent transcription rate dataset. By comparing this dataset with the indirect ones obtained from the mRNA stabilities and mRNA amount datasets, we are able to obtain biological information about posttranscriptional regulation processes and a genomic snapshot of the location of the active transcriptional machinery. We have obtained nascent transcription rates for 4,670 yeast genes. The median RNA polymerase II density in the genes is 0.078 molecules/kb, which corresponds to an average of 0.096 molecules/gene. Most genes have transcription rates of between 2 and 30 mRNAs/hour and less than 1% of yeast genes have >1 RNA polymerase molecule/gene. Histone and ribosomal protein genes are the highest transcribed groups of genes and other than these exceptions the transcription of genes is an infrequent phenomenon in a yeast cell.
Walking Pattern Generation of a Biped Walking Vehicle Using a Dynamic Human Model

This paper describes a passive dynamic model of passenger for a biped walking vehicle. The walking pattern generation that enables stable walking even if passenger sits naturally is also described. The model consists of lower-limbs part assumed to be fixed to the robot, and the upper body assumed to be 1 particle with 2 DOF mounted on the seat via 2 springs and dampers. The parameters are identified through waist shaking experiments by using a force-torque sensor under the seat. The walking pattern generation method involves the proposed model being built onto a strict model of the robot, and through iteration computation, a stable walking pattern is generated. The effectiveness of the proposed method is confirmed through experiments
Dietary Diversity, Diet Cost, and Incidence of Type 2 Diabetes in the United Kingdom: A Prospective Cohort Study

Background Diet is a key modifiable risk factor for multiple chronic conditions, including type 2 diabetes (T2D). Consuming a range of foods from the five major food groups is advocated as critical to healthy eating, but the association of diversity across major food groups with T2D is not clear and the relationship of within-food-group diversity is unknown. In addition, there is a growing price gap between more and less healthy foods, which may limit the uptake of varied diets. The current study had two aims: first, to examine the association of reported diversity of intake of food groups as well as their subtypes with risk of developing T2D, and second, to estimate the monetary cost associated with dietary diversity. Methods and Findings A prospective study of 23,238 participants in the population-based EPIC-Norfolk cohort completed a baseline Food Frequency Questionnaire in 1993–1997 and were followed up for a median of 10 y. We derived a total diet diversity score and additional scores for diversity within each food group (dairy products, fruits, vegetables, meat and alternatives, and grains). We used multivariable Cox regression analyses for incident diabetes (892 new cases), and multivariable linear regression for diet cost. Greater total diet diversity was associated with 30% lower risk of developing T2D (Hazard ratio [HR] 0.70 [95% CI 0.51 to 0.95]) comparing diets comprising all five food groups to those with three or fewer, adjusting for confounders including obesity and socioeconomic status. In analyses of diversity within each food group, greater diversity in dairy products (HR 0.61 [0.45 to 0.81]), fruits (HR 0.69 [0.52 to 0.90]), and vegetables (HR 0.67 [0.52 to 0.87]) were each associated with lower incident diabetes. The cost of consuming a diet covering all 5 food groups was 18% higher (£4.15/day [4.14 to 4.16]) than one comprising three or fewer groups. Key limitations are the self-reported dietary data and the binary scoring approach whereby some food groups contained both healthy and less healthy food items. Conclusions A diet characterized by regular consumption of all five food groups and by greater variety of dairy, fruit, and vegetable subtypes, appears important for a reduced risk of diabetes. However, such a diet is more expensive. Public health efforts to prevent diabetes should include food price policies to promote healthier, more varied diets.
Role of the caspase-1 inflammasome in Salmonella typhimurium pathogenesis

Caspase-1 is activated by a variety of stimuli after the assembly of the “inflammasome,” an activating platform made up of a complex of the NOD-LRR family of proteins. Caspase-1 is required for the secretion of proinflammatory cytokines, such as interleukin (IL)-1β and IL-18, and is involved in the control of many bacterial infections. Paradoxically, however, its absence has been reported to confer resistance to oral infection by Salmonella typhimurium. We show here that absence of caspase-1 or components of the inflammasome does not result in resistance to oral infection by S. typhimurium, but rather, leads to increased susceptibility to infection.
THE REPLICATION OF DNA IN ESCHERICHIA COLI.

Studies of bacterial transformation and bacteriaphage infection1–5 strongly indicate that deoxyribonucleic acid (DNA) can carry and transmit hereditary information and can direct its own replication. Hypotheses for the mechanism of DNA replication differ in the predictions they make concerning the distribution among progeny molecules of atoms derived from parental molecules.6 Radioisotopic labels have been employed in experiments bearing on the distribution of parental atoms among progeny molecules in several organisms.6–9 We anticipated that a label which imparts to the DNA molecule an increased density might permit an analysis of this distribution by sedimentation techniques. To this end, a method was developed for the detection of small density differences among macromolecules.10 By use of this method, we have observed the distribution of the heavy nitrogen isotope N15 among molecules of DNA following the transfer of a uniformly N15-labeled, exponentially growing bacterial population to a growth medium containing the ordinary nitrogen isotope N14. A small amount of DNA in a concentrated solution of cesium chloride is centrifuged until equilibrium is closely approached. The opposing processes of sedimentation and diffusion have then produced a stable concentration gradient of the cesium chloride. The concentration and pressure gradients result in a continuous increase of density along the direction of centrifugal force. The macromolecules of DNA present in this density gradient are driven by the centrifugal field into the region where the solution density is equal to their own buoyant density.11 This concentrating tendency is opposed by diffusion, with the result that at equilibrium a single species of DNA is distributed over a band whose width is inversely related to the molecular weight of that species (Fig. 1). Fig. 1. Ultraviolet absorption photographs showing successive stages …
Minimum delay scheduling with multi-packet transmission in wireless networks

This paper studies the problem of minimum delay scheduling in wireless networks with multi-packet transmission capability. Specifically, we assume that the network employs superposition coding at the physical layer in order to implement multi-packet transmission. While most studies on superposition coding assume that unbounded number of packets can be coded together, physical and MAC layer limitations restrict the number of concurrent packets in a transmission set. Taking this constraint into consideration, we formulate the minimum delay scheduling as a combinatorial optimization problem and study its computational complexity under different transmission set sizes. We show that, when the transmission set size is limited to 2 packets, the problem can be solved optimally in polynomial time. Moreover, while the complexity of the problem for larger transmission set sizes is unknown, we present close-to-optimal heuristic algorithms that compute efficient solutions for the problem in polynomial time. Numerical results are also presented to study the efficiency and utility of the presented scheduling algorithms. Our results show that the heuristic algorithms are highly efficient, achieving delays that are less than 2% away from the optimal values.