Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine-Scale Bacterial Beta Diversity within a Complex Ecosystem (Zodletone Spring, OK, USA): The Role of the Rare Biosphere

Background The adaptation of pyrosequencing technologies for use in culture-independent diversity surveys allowed for deeper sampling of ecosystems of interest. One extremely well suited area of interest for pyrosequencing-based diversity surveys that has received surprisingly little attention so far, is examining fine scale (e.g. micrometer to millimeter) beta diversity in complex microbial ecosystems. Methodology/Principal Findings We examined the patterns of fine scale Beta diversity in four adjacent sediment samples (1mm apart) from the source of an anaerobic sulfide and sulfur rich spring (Zodletone spring) in southwestern Oklahoma, USA. Using pyrosequencing, a total of 292,130 16S rRNA gene sequences were obtained. The beta diversity patterns within the four datasets were examined using various qualitative and quantitative similarity indices. Low levels of Beta diversity (high similarity indices) were observed between the four samples at the phylum-level. However, at a putative species (OTU0.03) level, higher levels of beta diversity (lower similarity indices) were observed. Further examination of beta diversity patterns within dominant and rare members of the community indicated that at the putative species level, beta diversity is much higher within rare members of the community. Finally, sub-classification of rare members of Zodletone spring community based on patterns of novelty and uniqueness, and further examination of fine scale beta diversity of each of these subgroups indicated that members of the community that are unique, but non novel showed the highest beta diversity within these subgroups of the rare biosphere. Conclusions/Significance The results demonstrate the occurrence of high inter-sample diversity within seemingly identical samples from a complex habitat. We reason that such unexpected diversity should be taken into consideration when exploring gamma diversity of various ecosystems, as well as planning for sequencing-intensive metagenomic surveys of highly complex ecosystems.
Specular reflection, gloss, roughness and surface heterogeneity of biopolymer coatings

The gloss values of biopolymer coatings were predicted by the Fresnel model from solid film refractive index measurements. Measured gloss properties of transparent coatings fit the model better than did those of wax- or lipid-dispersion coatings. Lipid content and particle size of dispersion coatings had a large influence on coating gloss. The effect of surface roughness on gloss was small compared with that of surface heterogeneity. Whey protein isolate and shellac coatings had higher gloss than hydroxypropyl methylcellulose coatings. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 79: 2221–2229, 2001
The Critical Role of Locomotion Mechanics in Decoding Sensory Systems

How do neural systems process sensory information to control locomotion? The weakly electric knifefish Eigenmannia, an ideal model for studying sensorimotor control, swims to stabilize the sensory image of a sinusoidally moving refuge. Tracking performance is best at stimulus frequencies less than ∼1 Hz. Kinematic analysis, which is widely used in the study of neural control of movement, predicts commensurately low-pass sensory processing for control. The inclusion of Newtonian mechanics in the analysis of the behavior, however, categorically shifts the prediction: this analysis predicts that sensory processing is high pass. The counterintuitive prediction that a low-pass behavior is controlled by a high-pass neural filter nevertheless matches previously reported but poorly understood high-pass filtering seen in electrosensory afferents and downstream neurons. Furthermore, a model incorporating the high-pass controller matches animal behavior, whereas the model with the low-pass controller does not and is unstable. Because locomotor mechanics are similar in a wide array of animals, these data suggest that such high-pass sensory filters may be a general mechanism used for task-level locomotion control. Furthermore, these data highlight the critical role of mechanical analyses in addition to widely used kinematic analyses in the study of neural control systems.
Eryptosis as a marker of Parkinson's disease

A major trend in recent Parkinson's disease (PD) research is the investigation of biological markers that could help in identifying at-risk individuals or to track disease progression and response to therapies. Central to this is the knowledge that inflammation is a known hallmark of PD and of many other degenerative diseases. In the current work, we focus on inflammatory signalling in PD, using a systems approach that allows us to look at the disease in a more holistic way. We discuss cyclooxygenases, prostaglandins, thromboxanes and also iron in PD. These particular signalling molecules are involved in PD pathophysiology, but are also very important in an aberrant coagulation/hematology system. We present and discuss a hypothesis regarding the possible interaction of these aberrant signalling molecules implicated in PD, and suggest that these molecules may affect the erythrocytes of PD patients. This would be observable as changes in the morphology of the RBCs and of PD patients relative to healthy controls. We then show that the RBCs of PD patients are indeed rather dramatically deranged in their morphology, exhibiting eryptosis (a kind of programmed cell death). This morphological indicator may have useful diagnostic and prognostic significance.
Clinical characteristics and outcomes with rivaroxaban vs. warfarin in patients with non-valvular atrial fibrillation but underlying native mitral and aortic valve disease participating in the ROCKET AF trial

Aims We investigated clinical characteristics and outcomes of patients with significant valvular disease (SVD) in the Rivaroxaban Once Daily Oral Direct Factor Xa Inhibition Compared with Vitamin K Antagonism for Prevention of Stroke and Embolism Trial in Atrial Fibrillation (ROCKET AF) trial. Methods and results ROCKET AF excluded patients with mitral stenosis or artificial valve prostheses. We used Cox regression to adjust comparisons for potential confounders. Among 14 171 patients, 2003 (14.1%) had SVD; they were older and had more comorbidities than patients without SVD. The rate of stroke or systemic embolism with rivaroxaban vs. warfarin was consistent among patients with SVD [2.01 vs. 2.43%; hazard ratio (HR) 0.83, 95% confidence interval (CI) 0.55–1.27] and without SVD (1.96 vs. 2.22%; HR 0.89, 95% CI 0.75–1.07; interaction P = 0.76). However, rates of major and non-major clinically relevant bleeding with rivaroxaban vs. warfarin were higher in patients with SVD (19.8% rivaroxaban vs. 16.8% warfarin; HR 1.25, 95% CI 1.05–1.49) vs. those without (14.2% rivaroxaban vs. 14.1% warfarin; HR 1.01, 95% CI 0.94–1.10; interaction P = 0.034), even when controlling for risk factors and potential confounders. In intracranial haemorrhage, there was no interaction between patients with and without SVD where the overall rate was lower among those randomized to rivaroxaban. Conclusions Many patients with ‘non-valvular atrial fibrillation’ have significant valve lesions. Their risk of stroke is similar to that of patients without SVD after controlling for stroke risk factors. Efficacy of rivaroxaban vs. warfarin was similar in patients with and without SVD; however, the observed risk of bleeding was higher with rivaroxaban in patients with SVD but was the same among those without SVD. Atrial fibrillation patients with and without SVD experience the same stroke-preventive benefit of oral anticoagulants.
H2S Protects Against Pressure Overload–Induced Heart Failure via Upregulation of Endothelial Nitric Oxide Synthase

Background— Cystathionine &ggr;-lyase (CSE) produces H2S via enzymatic conversion of L-cysteine and plays a critical role in cardiovascular homeostasis. We investigated the effects of genetic modulation of CSE and exogenous H2S therapy in the setting of pressure overload–induced heart failure. Methods and Results— Transverse aortic constriction was performed in wild-type, CSE knockout, and cardiac-specific CSE transgenic mice. In addition, C57BL/6J or CSE knockout mice received a novel H2S donor (SG-1002). Mice were followed up for 12 weeks with echocardiography. We observed a >60% reduction in myocardial and circulating H2S levels after transverse aortic constriction. CSE knockout mice exhibited significantly greater cardiac dilatation and dysfunction than wild-type mice after transverse aortic constriction, and cardiac-specific CSE transgenic mice maintained cardiac structure and function after transverse aortic constriction. H2S therapy with SG-1002 resulted in cardioprotection during transverse aortic constriction via upregulation of the vascular endothelial growth factor–Akt–endothelial nitric oxide synthase–nitric oxide–cGMP pathway with preserved mitochondrial function, attenuated oxidative stress, and increased myocardial vascular density. Conclusions— Our results demonstrate that H2S levels are decreased in mice in the setting of heart failure. Moreover, CSE plays a critical role in the preservation of cardiac function in heart failure, and oral H2S therapy prevents the transition from compensated to decompensated heart failure in part via upregulation of endothelial nitric oxide synthase and increased nitric oxide bioavailability.
An Ada Interface for Application-Defined Scheduling

This paper presents an application program interface (API) that enables applications to use application-defined scheduling algorithms in a way compatible with the scheduling model of the Ada 95 Real-Time Systems Annex. Several application-defined schedulers, implemented as special user tasks, can coexist in the system in a predictable way. This API is currently implemented on our operating system MaRTE OS.
Lower bounds for randomized consensus under a weak adversary

This paper studies the inherent trade-off between termination probability and total step complexity of randomized consensus algorithms. It shows that for every integer k, the probability that an f-resilient randomized consensus algorithm of n processes does not terminate with agreement within k(n-f) steps is at least 1/ck, for some constant c. The lower bound holds for asynchronous systems, where processes communicate either by message passing or through shared memory, under a very weak adversary that determines the schedule in advance, without observing the algorithm's actions. This complements algorithms of Kapron et al. (SODA 2008), for message-passing systems, and of Aumann et al. (PODC 1997, Distributed Computing 2005), for shared-memory systems.
Aberrant Expression of Oncogenic and Tumor-Suppressive MicroRNAs in Cervical Cancer Is Required for Cancer Cell Growth

MicroRNAs (miRNAs) play important roles in cancer development. By cloning and sequencing of a HPV16+ CaSki cell small RNA library, we isolated 174 miRNAs (including the novel miR-193c) which could be grouped into 46 different miRNA species, with miR-21, miR-24, miR-27a, and miR-205 being most abundant. We chose for further study 10 miRNAs according to their cloning frequency and associated their levels in 10 cervical cancer- or cervical intraepithelial neoplasia-derived cell lines. No correlation was observed between their expression with the presence or absence of an integrated or episomal HPV genome. All cell lines examined contained no detectable miR-143 and miR-145. HPV-infected cell lines expressed a different set of miRNAs when grown in organotypic raft cultured as compared to monolayer cell culture, including expression of miR-143 and miR-145. This suggests a correlation between miRNA expression and tissue differentiation. Using miRNA array analyses for age-matched normal cervix and cervical cancer tissues, in combination with northern blot verification, we identified significantly deregulated miRNAs in cervical cancer tissues, with miR-126, miR-143, and miR-145 downregulation and miR-15b, miR-16, miR-146a, and miR-155 upregulation. Functional studies showed that both miR-143 and miR-145 are suppressive to cell growth. When introduced into cell lines, miR-146a was found to promote cell proliferation. Collectively, our data indicate that downregulation of miR-143 and miR-145 and upregulation of miR-146a play a role in cervical carcinogenesis.
Investigating the Role of the Melanocortin-1 Receptor Gene in an Extreme Case of Microgeographical Variation in the Pattern of Melanin-Based Plumage Pigmentation

The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such as POMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation. Trial Registration All sequences submitted to Genbank. Accession number: JX914505 to JX914564.
Application and Evaluation of the RF Charge-Pumping Technique

In this paper, we will discuss the extendibility of the charge-pumping (CP) technique toward frequencies up to 4 GHz. Such high frequencies are attractive when a significant gate leakage current flows, obscuring the CP current at lower pumping frequencies. It is shown that using RF gate excitation, accurate CP curves can be obtained on MOS devices with a leakage current density exceeding 1 Aldrcm-2. A theoretical analysis of the trap response to RF gate voltage signals is presented, giving a clear insight on the benefits and limitations of the technique.
Repeated adeno-associated virus serotype 2 aerosol-mediated cystic fibrosis transmembrane regulator gene transfer to the lungs of patients with cystic fibrosis: a multicenter, double-blind, placebo-controlled trial.

STUDY OBJECTIVES The primary objective was to determine the safety and tolerability of repeated doses of aerosolized adeno-associated serotype 2 vector containing cystic fibrosis transmembrane conductance regulator (CFTR) complementary DNA (cDNA) [tgAAVCF], an adeno-associated virus (AAV) vector encoding the complete human CFTR cDNA. Secondary objectives included evaluation of pulmonary function assessed by spirometry, lung abnormalities by high-resolution CT (HRCT), airway cytokines, vector shedding, serum neutralizing antibody to AAV serotype 2 (AAV2), and gene transfer and expression in a subset of subjects undergoing bronchoscopy with bronchial brushings. DESIGN Randomized, double-blind, placebo-controlled, phase II trial. SETTING Eight cystic fibrosis (CF) centers in the United States. SUBJECTS CF patients with mild lung disease, defined as FEV(1) > or =60% predicted. INTERVENTIONS Subjects were randomized to inhale three aerosolized doses of 1 x 10(13) deoxyribonuclease-resistant particles of tgAAVCF or matching placebo at 30-day intervals using the Pari LC Plus nebulizer (PARI; Richmond, VA). MEASUREMENTS AND RESULTS Of 42 subjects randomized, 20 subjects received at least one dose of tgAAVCF and 17 subjects received placebo. No difference in the pattern of adverse events or laboratory abnormalities was noted between the two treatment groups. Improvements in induced-sputum interleukin-8 (p = 0.03) and FEV(1) (p = 0.04) were observed at day 14 and day 30, respectively, in the group receiving tgAAVCF when compared to those receiving placebo. No significant differences in HRCT scans were noted. Vector shedding in sputum was observed at low levels up to 90 days after the third dose of vector. All subjects receiving tgAAVCF exhibited an increase (by at least fourfold) in serum AAV2-neutralizing antibodies and detectable levels in BAL fluid from five of six treated subjects undergoing BAL. Gene transfer but not gene expression was detected in a subset of six tgAAVCF subjects who underwent bronchoscopy. CONCLUSIONS Repeat doses of aerosolized tgAAVCF were safe and well tolerated, and resulted in encouraging trends in improvement in pulmonary function in patients with CF and mild lung disease.
Underwater Data Collection Using Robotic Sensor Networks

We examine the problem of utilizing an autonomous underwater vehicle (AUV) to collect data from an underwater sensor network. The sensors in the network are equipped with acoustic modems that provide noisy, range-limited communication. The AUV must plan a path that maximizes the information collected while minimizing travel time or fuel expenditure. We propose AUV path planning methods that extend algorithms for variants of the Traveling Salesperson Problem (TSP). While executing a path, the AUV can improve performance by communicating with multiple nodes in the network at once. Such multi-node communication requires a scheduling protocol that is robust to channel variations and interference. To this end, we examine two multiple access protocols for the underwater data collection scenario, one based on deterministic access and another based on random access. We compare the proposed algorithms to baseline strategies through simulated experiments that utilize models derived from experimental test data. Our results demonstrate that properly designed communication models and scheduling protocols are essential for choosing the appropriate path planning algorithms for data collection.
Value-based decision making via sequential sampling with hierarchical competition and attentional modulation

In principle, formal dynamical models of decision making hold the potential to represent fundamental computations underpinning value-based (i.e., preferential) decisions in addition to perceptual decisions. Sequential-sampling models such as the race model and the drift-diffusion model that are grounded in simplicity, analytical tractability, and optimality remain popular, but some of their more recent counterparts have instead been designed with an aim for more feasibility as architectures to be implemented by actual neural systems. Connectionist models are proposed herein at an intermediate level of analysis that bridges mental phenomena and underlying neurophysiological mechanisms. Several such models drawing elements from the established race, drift-diffusion, feedforward-inhibition, divisive-normalization, and competing-accumulator models were tested with respect to fitting empirical data from human participants making choices between foods on the basis of hedonic value rather than a traditional perceptual attribute. Even when considering performance at emulating behavior alone, more neurally plausible models were set apart from more normative race or drift-diffusion models both quantitatively and qualitatively despite remaining parsimonious. To best capture the paradigm, a novel six-parameter computational model was formulated with features including hierarchical levels of competition via mutual inhibition as well as a static approximation of attentional modulation, which promotes “winner-take-all” processing. Moreover, a meta-analysis encompassing several related experiments validated the robustness of model-predicted trends in humans’ value-based choices and concomitant reaction times. These findings have yet further implications for analysis of neurophysiological data in accordance with computational modeling, which is also discussed in this new light.
Who's in control?: exploring human-agent interaction in the McPie interactive theater project

The McPie Interactive Theater project explores an unusual style of interaction between human users and visual software agents. Unlike direct manipulation or intelligent agents, McPie explicitly creates a co-adaptive interaction, in which both the human user and the agent modify their behavior according to a changing set of criteria with respect to the other's behavior. The final implementation was tested at an Interactive Theater exhibition in front of a live audience over three days. Volunteers wearing motion detection equipment, interacted with McPie, an animated 3d character back-projected on a wall-sized screen. The setting offered a rich environment for trying out otherwise-controversial interaction styles and suggests new directions for human-agent interaction.
Positive Correlation between Virulence ofPseudomonas aeruginosa Mutants in Mice and Insects

ABSTRACT Strain PA14, a human clinical isolate of Pseudomonas aeruginosa, is pathogenic in mice and insects (Galleria mellonella). Analysis of 32 different PA14 mutants in these two hosts showed a novel positive correlation in the virulence patterns. Thus, G. mellonella is a good model system for identifying mammalian virulence factors of P. aeruginosa.
Understanding the Motivation of Contribution in Online Communities An Empirical Investigation of an Online Travel Community

This study intends to contribute to the understanding of online community by empirically answering the question of why community members are willing to making active contributions to their community. The relationships between members perceived importance of contribution motivation and their level of contribution in online communities are identified. In addition, the results of factor analysis and reliability tests indicate that the proposed conceptual framework is valid and can serve as a basis for the understanding of online community members motivation of contribution. The results of the regression analysis show that efficacy, instrumental, and expectancy have positive effects on level of contribution. Discussion and implications are provided based on the study results.
Atomic mobility and fast crystallization of the phase change compound GeTe

The application of amorphous chalcogenide alloys as phase change materials in data-storage media rests on their ability to undergo an extremely fast (10-100 ns) crystallization upon heating. What makes these materials so special in this respect is, however, still a matter of debate. By means of large scale molecular dynamics simulations, we demonstrate that the phase change compound GeTe shows a high atomic mobility in the amorphous phase overheated just above the glass transition temperature. This behavior leads to a breakdown of the Stokes-Einstein relation between the selfdiffusion coefficient and the viscosity which is one of the keys to understand the fast crystallization of materials in this class.