Miracle-dz/UniFAR-FTUs huggingface dataset:
Experimental Manipulation Shows a Greater Influence of Population than Dietary Perturbation on the Microbiome of Tyrophagus putrescentiae

ABSTRACT Tyrophagus putrescentiae is inhabited by bacteria that differ among mite populations (strains) and diets. Here, we investigated how the microbiome and fitness of T. putrescentiae are altered by dietary perturbations and mite populations. Four T. putrescentiae populations, referred to as dog, Koppert, laboratory, and Phillips, underwent a perturbation, i.e., a dietary switch from a rearing diet to two experimental diets. The microbiome was investigated by sequencing the V1-V3 portion of the 16S rRNA gene, and selected bacterial taxa were quantified by quantitative PCR (qPCR) using group/taxon-specific primers. The parameters observed were the changes in mite population growth and nutritional status, i.e., the total glycogen, lipid, saccharide, and protein contents in mites. The effect of diet perturbation on the variability of the microbiome composition and population growth was lower than the effect induced by mite population. In contrast, the diet perturbation showed a greater effect on nutritional status of mites than the mite population. The endosymbionts exhibited high variations among T. putrescentiae populations, including Cardinium in the laboratory population, Blattabacterium-like bacteria in the dog population, and Wolbachia in the dog and Phillips populations. Solitalea-like and Bartonella-like bacteria were present in the dog, Koppert, and Phillips populations in different proportions. The T. putrescentiae microbiome is dynamic and varies based on both the mite population and perturbation; however, the mites remain characterized by robust bacterial communities. Bacterial endosymbionts were found in all populations but represented a dominant portion of the microbiome in only some populations. IMPORTANCE We addressed the question of whether population origin or perturbation exerts a more significant influence on the bacterial community of the stored product mite Tyrophagus putrescentiae. The microbiomes of four populations of T. putrescentiae insects subjected to diet perturbation were compared. Based on our results, the bacterial community was more affected by the mite population than by diet perturbation. This result can be interpreted as indicating high stability of the putative intracellular symbionts in response to dietary perturbation. The changes in the absolute and relative numbers of Wolbachia, Blattabacterium-like, Solitalea-like, and Cardinium bacteria in the T. putrescentiae populations can also be caused by neutral processes other than perturbation. When nutritional status is considered, the effect of population appeared less important than the perturbation. We hypothesize that differences in the proportions of the endosymbiotic bacteria result in changes in mite population growth.
Whistle: Synchronization-Free TDOA for Localization

Localization is of great importance in mobile and wireless network applications. TDOA is one of the widely used localization schemes, in which a to-be located object emits a signal and a number of receivers record the arriving time of the signal. By calculating the time difference of different receivers, the location of the object is estimated. In such a scheme, receivers must be precisely synchronized, even slight noises are completely unacceptable for centimeter-level localization. Previous studies have shown that existing time synchronization approaches for low-cost devices are insufficiently accurate and basically infeasible for high accuracy localization. In our scheme (called Whistle), several asynchronous receivers record a target signal and a successive signal that is generated artificially. By two-signal sensing and sample counting techniques, high time resolution can be achieved. This design fundamentally changes TDOA in the sense of releasing the synchronization requirement and avoiding many sources of inaccuracy. We implement Whistle on commercial off-the-shelf (COTS) cell phones. Through extensive real-world experiments in indoor and outdoor, quiet and noisy environments, the mean error is 10~20 centimeters in a 9m ˜ 9m ˜ 4m_3 3D space.
Dynamic Contract Design for Heterogenous Workers in Crowdsourcing for Quality Control

Crowdsourcing sites heavily rely on paid workers to ensure completion of tasks. Yet, designing a pricing strategies able to incentivize users' quality and retention is non trivial. Existing payment strategies either simply set a fixed payment per task without considering changes in workers' behaviors, or rule out poor quality responses and workers based on coarse criteria. Hence, task requesters may be investing significantly in work that is inaccurate or even misleading. In this paper, we design a dynamic contract to incentivize high-quality work. Our proposed approach offers a theoretically proven algorithm to calculate the contract for each worker in a cost-efficient manner. In contrast to existing work, our contract design is not only adaptive to changes in workers' behavior, but also adjusts pricing policy in the presence of malicious behavior. Both theoretical and experimental analysis over real Amazon review traces show that our contract design can achieve a near optimal solution. Furthermore, experimental results demonstrate that our contract design 1) can promote high-quality work and prevent malicious behavior, and 2) outperforms the intuitive strategy of excluding all malicious workers in terms of the requester's utility.
Perspectives on Intravenous Oxycodone for Control of Postoperative Pain

Intravenous (IV) analgesia has particular advantages in the immediate postoperative period. For example, IV administration results in a faster onset of pain relief and results in more predictable pharmacokinetics than does administration by other routes. It also allows for convenient dosing before or during surgery, permitting the initiation of effective analgesia in the early phase of the postoperative period. In addition, when patients are able to tolerate oral intake, they can be switched from IV to oral dosing based on maintaining the predictable analgesia established by the IV route. IV morphine is widely used for the control of postoperative pain, but there is a trend toward the use of oxycodone. Oxycodone (which may be mediated partly through kappa‐ as well as mu‐opioid receptors) offers several potential advantages. Published studies comparing IV oxycodone to other IV opioids for postsurgical pain report that oxycodone is a safe and effective analgesic. Some studies show that IV oxycodone may be associated with greater pain control, fewer or less severe adverse events, and faster onset of action, although the results are not consistent across all studies. Oxycodone has been reported to be safe in the geriatric and other special populations when adequate clinical adjustments are made. Thus, the clinical reports and oxycodone's pharmacologic profile make intravenous oxycodone a potentially important “new” old drug for postoperative pain control.
Metabolism of myo-Inositol by Legionella pneumophila Promotes Infection of Amoebae and Macrophages

ABSTRACT Legionella pneumophila is a natural parasite of environmental amoebae and the causative agent of a severe pneumonia termed Legionnaires' disease. The facultative intracellular pathogen employs a bipartite metabolism, where the amino acid serine serves as the major energy supply, while glycerol and glucose are mainly utilized for anabolic processes. The L. pneumophila genome harbors the cluster lpg1653 to lpg1649 putatively involved in the metabolism of the abundant carbohydrate myo-inositol (here termed inositol). To assess inositol metabolism by L. pneumophila, we constructed defined mutant strains lacking lpg1653 or lpg1652, which are predicted to encode the inositol transporter IolT or the inositol-2-dehydrogenase IolG, respectively. The mutant strains were not impaired for growth in complex or defined minimal media, and inositol did not promote extracellular growth. However, upon coinfection of Acanthamoeba castellanii, the mutants were outcompeted by the parental strain, indicating that the intracellular inositol metabolism confers a fitness advantage to the pathogen. Indeed, inositol added to L. pneumophila-infected amoebae or macrophages promoted intracellular growth of the parental strain, but not of the ΔiolT or ΔiolG mutant, and growth stimulation by inositol was restored by complementation of the mutant strains. The expression of the P iol promoter and bacterial uptake of inositol required the alternative sigma factor RpoS, a key virulence regulator of L. pneumophila. Finally, the parental strain and ΔiolG mutant bacteria but not the ΔiolT mutant strain accumulated [U-14C6]inositol, indicating that IolT indeed functions as an inositol transporter. Taken together, intracellular L. pneumophila metabolizes inositol through the iol gene products, thus promoting the growth and virulence of the pathogen. IMPORTANCE The environmental bacterium Legionella pneumophila is the causative agent of a severe pneumonia termed Legionnaires' disease. The opportunistic pathogen replicates in protozoan and mammalian phagocytes in a unique vacuole. Amino acids are thought to represent the prime source of carbon and energy for L. pneumophila. However, genome, transcriptome, and proteome studies indicate that the pathogen not only utilizes amino acids as carbon sources but possesses broader metabolic capacities. In this study, we analyzed the metabolism of inositol by extra- and intracellularly growing L. pneumophila. By using genetic, biochemical, and cell biological approaches, we found that L. pneumophila accumulates and metabolizes inositol through the iol gene products, thus promoting the intracellular growth, virulence, and fitness of the pathogen. Our study significantly contributes to an understanding of the intracellular niche of a human pathogen.
Improving the Immersion in Virtual Reality with Real-Time Avatar and Haptic Feedback in a Cricket Simulation

The basis of this research is concerned with designing and implementing a system that allows a player to engage in a virtual reality (VR) game with better immersion. The research was based on the idea that an avatar generated using real-time motion capture would improve the player’s immersion by increasing the perception of presence. When playing the VR games a common problem was observed. The user’s avatar (Virtual agent) was not improved as most of the games were played using limited controllers. The inputs from these controllers were noted as insufficient to generate the entire body’s animation. This research attempts to solve this problem by proposing/implementing full body motion capture and the establishment of the self-avatar in real time in a VR game. This involved designing a system that utilizes the effective technologies for 3D imaging, transmission and haptic feedback. The research attempts to measure the immersion by enhancing measuring instruments (Norman, 2010). It is complimented by a user-based study that involves/involved collecting both qualitative and quantitative data through questionnaire and observation.
COPD-associated pulmonary hypertension: clinical implications and current methods for treatment

ABSTRACT Introduction: Chronic obstructive pulmonary disease is the fourth leading cause of death worldwide, one serious complication being pulmonary hypertension, which occurs in up to 30% of patients and increases mortality drastically. Difficulties in diagnosis and the unclear beneficial effects of PH-specific therapy have hitherto resulted in the absence of approved therapies. Consequently, PH and right heart failure in COPD are still currently treated according to symptoms and not underlying cause Areas covered: This review focuses on the current knowledge of its pathogenesis, clinical picture, diagnosis as well as methods for treatment Expert commentary: Since PH-COPD is an orphan disease with grievous consequences, and diagnosis as well as the right choice of possible treatment is crucial, referral to an expert center in cases of suspicion is necessary. Hitherto there is no officially approved treatment available even though several studies have shown notable improvement in selected individuals, making diagnostics, prognostic markers, and the search for therapeutic agents key issues of interest in this field.
Pulmonary Artery Enlargement Is Associated With Right Ventricular Dysfunction and Loss of Blood Volume in Small Pulmonary Vessels in Chronic Obstructive Pulmonary Disease

Background—Chronic obstructive pulmonary disease causes significant morbidity and concomitant pulmonary vascular disease and cardiac dysfunction are associated with poor prognosis. Computed tomography–detected relative pulmonary artery (PA) enlargement defined as a PA to ascending aorta diameter ratio >1 (PA:A>1) is a marker for pulmonary hypertension and predicts chronic obstructive pulmonary disease exacerbations. However, little is known about the relationship between the PA:A ratio, pulmonary blood volume, and cardiac function. Methods and Results—A single-center prospective cohort study of patients with chronic obstructive pulmonary disease was conducted. Clinical characteristics and computed tomography metrics, including the PA:A and pulmonary blood vessel volume, were measured. Ventricular functions, volumes, and dimensions were measured by cine cardiac MRI with 3-dimensional analysis. Linear regression examined the relationships between clinical characteristics, computed tomography and cardiac MRI metrics, and 6-minute walk distance. Twenty-four patients were evaluated and those with PA:A>1 had higher right ventricular (RV) end-diastolic and end-systolic volume indices accompanied by lower RV ejection fraction (52±7% versus 60±9%; P=0.04). The PA:A correlated inversely with total intraparenchymal pulmonary blood vessel volume and the volume of distal vessels with a cross-sectional area of <5 mm2. Lower forced expiratory volume, PA:A>1, and hyperinflation correlated with reduced RV ejection fraction. Both PA diameter and reduced RV ejection fraction were independently associated with reduced 6-minute walk distance. Conclusions—The loss of blood volume in distal pulmonary vessels is associated with PA enlargement on computed tomography. Cardiac MRI detects early RV dysfunction and remodeling in nonsevere chronic obstructive pulmonary disease patients with a PA:A>1. Both RV dysfunction and PA enlargement are independently associated with reduced walk distance. Clinical Trial Registration—URL: http://www.clinicaltrials. gov. Unique identifier: NCT00608764.
The lost language of the RNA World

RNA-derived signaling molecules in modern cells may represent evolutionary vestiges of a time when all cellular functions were performed by RNAs. Gloss The discovery of numerous riboswitch classes reveals that many of these RNA structures regulate gene expression in response to the selective binding of coenzymes and signaling molecules derived from RNA monomers or their precursors. It has been proposed that many coenzymes might be of ancient origin, based on their universal distribution in biology and their RNA-like chemical composition. In this Review, which includes four figures and 103 references, we discuss the findings that support the hypothesis that common RNA-derived signaling compounds are ancient and speculate on the possible complexity of the chemical language that might have been used by life-forms long before proteins emerged. The possibility of an RNA World is based on the notion that life on Earth passed through a primitive phase without proteins, a time when all genomes and enzymes were composed of ribonucleic acids. Numerous apparent vestiges of this ancient RNA World remain today, including many nucleotide-derived coenzymes, self-processing ribozymes, metabolite-binding riboswitches, and even ribosomes. Many of the most common signaling molecules and second messengers used by modern organisms are also formed from RNA nucleotides or their precursors. For example, nucleotide derivatives such as cAMP, ppGpp, and ZTP, as well as the cyclic dinucleotides c-di-GMP and c-di-AMP, are intimately involved in signaling diverse physiological or metabolic changes in bacteria and other organisms. We describe the potential diversity of this "lost language" of the RNA World and speculate on whether additional components of this ancient communication machinery might remain hidden though still very much relevant to modern cells.
A PHOC Decoder for Lexicon-Free Handwritten Word Recognition

In this paper, we propose a novel probabilistic model for lexicon-free handwriting recognition. Model inputs are word images encoded as Pyramidal Histogram Of Character (PHOC) vectors. PHOC vectors have been used as efficient attribute-based, multi-resolution representations of either text strings or word image contents. The proposed model formulates PHOC decoding as the problem of finding the most probable sequence of characters corresponding to the given PHOC. We model PHOC layers as Beta-distributed observations, linked to hidden states that correspond to character estimates. Characters are in turn linked to one another along a Markov chain, encoding language model information. The sequence of characters is estimated using the max-sum algorithm in a process that is akin to Viterbi decoding. Numerical experiments on the well-known George Washington database show competitive recognition results.
GRASP based metaheuristics for layout pattern classification

Layout pattern classification has been recently utilized in IC design. It clusters hotspot patterns for design-space analysis or yield optimization. In pattern classification, an optimal clustering is essential, as well as its runtime and accuracy. Within the research-oriented infrastructure used in the ICCAD 2016 contest, we have developed a fast metaheuristic for the pattern classification that utilizes the Greedy Randomized Adaptive Search Procedure (GRASP). Our proposed metaheuristic outperforms the best-reported results on all of the ICCAD 2016 benchmarks. In addition, we achieve up to a 50% cluster count reduction, and improve a runtime significantly compared to a commercial EDA tool provided in the ICCAD 2016 contest [1].
Evaluation of Alteration in Hepatic and Intestinal BCRP Function In Vivo from ABCG2 c.421C>A Polymorphism Based on PBPK Analysis of Rosuvastatin

Polymorphism c.421C>A in the ABCG2 gene is thought to reduce the activity of breast cancer resistance protein (BCRP), a xenobiotic transporter, although it is not clear which organ(s) contributes to the polymorphism-associated pharmacokinetic change. The aim of the present study was to estimate quantitatively the influence of c.421C>A on intestinal and hepatic BCRP activity using a physiologically based pharmacokinetic (PBPK) model of rosuvastatin developed from clinical data and several in vitro studies. Simultaneous fitting of clinical data for orally and intravenously administered rosuvastatin, obtained in human subjects without genotype information, was first performed with the PBPK model to estimate intrinsic clearance for hepatic elementary process. The fraction of BCRP activity in 421CA and 421AA (fca and faa values, respectively) with respect to that in 421CC subjects was then estimated based on extended clearance concepts and simultaneous fitting to oral administration data for the three genotypes (421CC, 421CA, and 421AA). On the assumption that c.421C>A affects both intestinal and hepatic BCRP, clinical data in each genotype were well reproduced by the model, and the estimated terminal half-life was compatible with the observed values. The assumption that c.421C>A affects only either intestinal or hepatic BCRP gave poorer agreement with observed values. The faa values obtained on the former assumption were 0.48–0.54. Thus, PBPK model analysis enabled quantitative evaluation of alteration in BCRP activity owing to c.421C>A, and BCRP activity in 421AA was estimated as half that in 421CC.
Design for Moment Redistribution in RC Beams Retrofitted with Steel Plates

It is now common practice to retrofit reinforced concrete members by adhesively bonding steel or fibre reinforced polymer plates to their surfaces. However, tests have shown that these plated RC structures tend to have less member ductility, or rotational capacity, than the unplated structure because of premature plate debonding. In this paper, structural mechanics approaches are described for both: quantifying the moment rotation capacity, or member ductility, of steel plated RC flexural members; and quantifying the moment redistribution capacity from the moment rotation capacity. It is shown how the moment redistribution structural mechanics model can be used to design for member ductility directly and, furthermore, it is applied to both externally bonded and near surface mounted steel plates. As would be expected, it is shown that steel plating produces more ductile members than fibre reinforced polymer plating.
Modeling the Gas Flow in the Bar of NGC 1365

We present new observations of the strongly barred galaxy NGC 1365, including new photometric images and Fabry-Perot spectroscopy, as well as a detailed reanalysis of the neutral hydrogen observations from the VLA archive. We find the galaxy to be at once remarkably bisymmetric in its I-band light distribution and strongly asymmetric in the distribution of dust and in the kinematics of the gas in the bar region. The velocity field mapped in the Hα line reveals bright H II regions with velocities that differ by 60-80 km s−1 from that of the surrounding gas, which may be due to remnants of infalling material. We have attempted hydrodynamic simulations of the bar flow to estimate the separate disk and halo masses, using two different dark matter halo models and covering a wide range of mass-to-light ratios (ϒ) and bar pattern speeds (Ωp). None of our models provides a compelling fit to the data, but they seem most nearly consistent with a fast bar, corotation at ~1.2rB, and ΥI≃ 2.0 ± 1.0, implying a massive, but not fully maximal, disk. The fitted dark halos are unusually concentrated, a requirement driven by the declining outer rotation curve.
The Agenda of Wearable Healthcare

Driven by cost and quality issues, the health system in the developed countries will undergo a fundamental change in this decade, from a physician-operated and hospital centred health system to consumer operated personal prevention, early risk detection and wellness system. This paper sketches the vision of a ‘Personal Health Assistant’ PHA, opening up new vistas in patient centred healthcare. The PHA comprises a wearable sensing and communicating system, seamlessly embedded in our daily outfit. Several onbody sensors identify the biometric and contextual status of the wearer continuously. The embedded computer generates the ‘Life Balance Factor’ LBF as an individual feedback to the user and to the surroundings affording an effective prevention, disease management and rehabilitation also in telemedicine. The state-of-the-art enabling technologies – mainly miniaturization of electronics and sensors combined with wireless communication and recent developments in wearable and pervasive computing are presented and assessed concerning multiparameter health monitoring.