Miracle-dz/UniFAR-FTUs huggingface dataset:
Plasmid-Encoded Traits Vary across Environments

Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. ABSTRACT Plasmids are key mobile genetic elements in bacterial evolution and ecology as they allow the rapid adaptation of bacteria under selective environmental changes. However, the genetic information associated with plasmids is usually considered separately from information about their environmental origin. To broadly understand what kinds of traits may become mobilized by plasmids in different environments, we analyzed the properties and accessory traits of 9,725 unique plasmid sequences from a publicly available database with known bacterial hosts and isolation sources. Although most plasmid research focuses on resistance traits, such genes made up <1% of the total genetic information carried by plasmids. Similar to traits encoded on the bacterial chromosome, plasmid accessory trait compositions (including general Clusters of Orthologous Genes [COG] functions, resistance genes, and carbon and nitrogen genes) varied across seven broadly defined environment types (human, animal, wastewater, plant, soil, marine, and freshwater). Despite their potential for horizontal gene transfer, plasmid traits strongly varied with their host’s taxonomic assignment. However, the trait differences across environments of broad COG categories could not be entirely explained by plasmid host taxonomy, suggesting that environmental selection acts on the plasmid traits themselves. Finally, some plasmid traits and environments (e.g., resistance genes in human-related environments) were more often associated with mobilizable plasmids (those having at least one detected relaxase) than others. Overall, these findings underscore the high level of diversity of traits encoded by plasmids and provide a baseline to investigate the potential of plasmids to serve as reservoirs of adaptive traits for microbial communities. IMPORTANCE Plasmids are well known for their role in the transmission of antibiotic resistance-conferring genes. Beyond human and clinical settings, however, they disseminate many other types of genes, including those that contribute to microbially driven ecosystem processes. In this study, we identified the distribution of traits genetically encoded by plasmids isolated from seven broadly categorized environments. We find that plasmid trait content varied with both bacterial host taxonomy and environment and that, on average, half of the plasmids were potentially mobilizable. As anthropogenic activities impact ecosystems and the climate, investigating and identifying the mechanisms of how microbial communities can adapt will be imperative for predicting the impacts on ecosystem functioning.
Pain Treatment and Cancer Patients: Are we Heeding Quality of Life?

Abstract The use of opioid analgesics remains the primary therapy for pain control in cancer patients. However, ample evidence persists showing that treatment is still inadequate. This cross-sectional study was carried out during one year in a Brazilian Cancer Hospital to evaluate the impact of opioid use on analgesia and patients’ quality of life. The Pain Management Index (PMI), EORTC QLQ.C30 (Quality of Life of Cancer Patients), Karnofsky Performance Status (KPS), Douleur Neuropathique 4 (DN4), and Brief Pain Inventory-Short Form (BPI-SF) were used. A hundred patients with advanced solid tumors and using opioids were included, with 82% of them reporting daily pain with 58% having intense pain. Morphine with a mean dose of 49 Morphine Milligram Equivalent were used by 57% of them, and PMI was negative in 34% of the sample. Neuropathic pain was found in 72% of patients. The pain was related to all BPI variables. Despite the substantial negative impact of pain on QOL, no association was found between the clinical factors assessed and QOL itself. This gap can be related to the persistence of high levels of sub-treatment, depression, and neuropathic pain associated with the use of low doses of opiates and adjuvant medications in the sample.
Application of iontophoresis in ophthalmic practice: an innovative strategy to deliver drugs into the eye

Abstract Delivery of drugs to special locations of ocular lesions, while minimizing systemic and local toxic effects, is recognized as a critical challenge in the ophthalmic practice. The special anatomy and physiology barriers within the eyeball entail effective drug delivery systems. Emerging attempts in drug delivery has led to developments in ocular iontophoresis, which acts as a noninvasive technology to enhance drug penetration using a small electric current. This technique offers greater flexibility to deliver desired drug dose in a controlled and tolerable manner. In previous studies, this technique has been testified to deliver antibiotics, corticoid, proteins and other gene drugs into the eye with the potency of treating or alleviating diverse ophthalmological diseases including uveitis, cataract, retinoblastoma, herpes simplex and cytomegalovirus retinitis (CMVR), etc. In this review, we will introduce the recent developments in iontophoresis device. We also summarize the latest progress in coulomb controlled iontophoresis (CCI), hydrogel ionic circuit (HIC) and EyeGate II delivery system (EGDS), as well as overview the potential toxicity of iontophoresis. We will discuss these factors that affect the efficacy of iontophoresis experiments, and focus on the latest progress in its clinical application in the treatment of eye diseases.
On the robust stability of a Clarke-Gawthrop type of self-tuning controller

In this paper the Clarke-Gawthrop type of self-tuning controller is modified and shown to be robust stable with respect to unmodelled plant uncertainties and bounded disturbances. A self-tuning controller is proposed here consisting of two steps: the first, an optimal control law, is derived by means of minimizing a quadratic cost function of the Clarke-Gawthrop type; the second, the optimal control law, is modified by introducing an estimate of the modelling error as a feedback. For the parameter estimation, a modified least-squares scheme with a relative dead zone is employed. The robustness results are derived by neither requiring too much a priori knowledge of the plant parameters, nor using any assumptions about the adaptive signals.
Hepatocyte-to-cholangiocyte conversion occurs through transdifferentiation independently of proliferation in zebrafish

Background and aims: Injury to biliary epithelial cells (BECs) lining the hepatic bile ducts leads to cholestatic liver diseases. Upon severe biliary damage, hepatocytes can convert to BECs, thereby contributing to liver recovery. Given a potential of augmenting this hepatocyte-to-BEC conversion as a therapeutic option for cholestatic liver diseases, it will be important to thoroughly understand the cellular and molecular mechanisms of the conversion process. Approach and results: Towards this aim, we have established a zebrafish model for hepatocyte-to-BEC conversion by employing Tg(fabp10a:CFP-NTR) zebrafish with a temporal inhibition of Notch signaling during regeneration. Cre/loxP-mediated permanent and H2B-mCherry-mediated short-term lineage tracing revealed that in the model, all BECs originate from hepatocytes. During the conversion, BEC markers are sequentially induced in the order of Sox9b, Yap/Taz, Notch activity/epcam, and Alcama/krt18; the expression of the hepatocyte marker Bhmt disappears between the Sox9b and Yap/Taz induction. Importantly, live time-lapse imaging unambiguously revealed transdifferentiation of hepatocytes into BECs: hepatocytes convert to BECs without transitioning through a proliferative intermediate state. In addition, using compounds and transgenic and mutant lines that modulate Notch and Yap signaling, we found that both Notch and Yap signaling are required for the conversion even in Notch- and Yap-overactivating settings. Conclusions: Hepatocyte-to-BEC conversion occurs through transdifferentiation independently of proliferation, and Notch and Yap signaling control the process in parallel with a mutually positive interaction. The new zebrafish model will further contribute to a thorough understanding of the mechanisms of the conversion process.
Content-aware three-dimensional image retargeting for mobile devices

We propose a novel content-aware three dimensional (3-D) image (two dimensional (2-D)-plus-depth) retargeting method using a 3-D saliency-based energy function that effectively describes perceptual importance of objects in 3-D space. The 2-D and depth images are retargeted together by carving out collinear seam paths corresponding to the one having the least 3-D saliency energy. However, resizing individual objects in different ratios without depth modification can cause surface shape distortion of the 3-D objects. To minimize such distortion, depth values for the objects are adaptively remapped examining depth histogram change. Experimental results indicate that the proposed method can preserve structures of important objects in 3-D space much more effectively than conventional methods.
Model Reduction of Input-Output Dynamical Systems by Proper Orthogonal Decomposition

We performed a study based on an empirical-based model reduction technique known as balanced proper-orthogonal-decomposition (POD). The technique, applicable to nonlinear systems, yields a set of basis functions that spans a POD-based subspace capturing the essential input-output dynamics structure and projection of the original model on this subspace yields the balanced reduced-order model (BROM). In this study the performance of the BROM is compared to the original high-order linear model and the dependence on the sampling parameters is studied. Even with large number of snapshots, we show that at least 52 real states are needed for the BROM to produce good performance. The sampling frequency has to be high enough to cover twice of the high-frequency modes of interest. We develop a novel algorithm, which in linear systems is based on a direct decomposition of the discrete Hankel matrix. The algorithm serves as a generalized balanced POD scheme for input-output model reduction. The algorithm is especially e‐cient for reduced number of snapshots and it well-suits nonlinear systems since propagation of adjoint equation is not required. A single sample rate is found inadequate to cover both high and low-end frequencies. To reduce the number of snapshots signiflcantly, we show that multiple sampling rates improves performance dramatically.
Simulation of N-face InGaN-based p-i-n solar cells

GaN/InGaN p-i-n solar cells with N-face are simulated. In contrast to the detrimental effect of normal polarization, the internal electric field induced by reversed polarization enhances the efficiency of carrier collection by enlarging the energy band tilting to the favorable direction in the InGaN absorption layer. This beneficial effect becomes more remarkable when the indium composition of the InGaN absorption layer is higher.
Three‐dimensional test simulations of the outer radiation belt electron dynamics including electron‐chorus resonant interactions

[1] We present results from our three-dimensional (3-D) simulations using the Salammbo electron radiation belt physical model. We have run steady state and dynamic storm test case simulations to study the effect of electron-chorus resonant interactions on the radiation belt electron dynamics. When electron-chorus interactions are introduced in the code outside the plasmasphere, results show that a seed population with a kappa distribution and a characteristic energy of 2 keV is accelerated up to a few MeV in the outer radiation belt. MeV electron fluxes increase by an order of magnitude during high magnetic activity conditions especially near L* ∼ 5 and for equatorial mirroring particles. We have also performed a parametric study of various important parameters to investigate how our results could be influenced by the uncertainty that characterizes their values. Results of this study show that if we consider higher values of the radial diffusion coefficients, different initial states, and different boundary conditions, we always observe a peak in the L* profile of the MeV electrons when electron-chorus interactions are included.
Saccadic inhibition during free viewing in macaque monkeys.

Through the process of saccadic inhibition, visual events briefly suppress eye movements including microsaccades. In humans, saccadic inhibition has been shown to occur in response to the presentation of para-foveal or peripheral visual distractors during fixation and target-directed saccades, and to physical changes of behaviorally relevant visual objects. In monkeys performing tasks that controlled eye movements, saccadic inhibition of microsaccades and target-directed saccades has been shown. Using eye data from three previously published studies, we investigated how saccade rate changed while monkeys were presented with visual stimuli under conditions with loose or no viewing demands. In 2 conditions, animals passively sat while an LED lamp flashed or screen-wide images appeared in front of them. In the third condition, images were repeated semi-periodically while animals had to maintain their gaze within a wide rectangular area and detect oddballs. Despite animals not being required to maintain fixation nor make saccades to particular targets, the onset of visual events led to a temporary reduction of saccade rate across all conditions. Interestingly, saccadic inhibition was found at image offsets as well. These results show that saccadic inhibition occurs in monkeys during free viewing.
Dose reference level based on size-specific dose estimate (SSDE) and feasibility of deriving effective body diameter using tube current and time product (mAs) for adult chest and abdomen computed tomography (CT) procedures

This study aimed to establish dose reference level (NDRL SSDE ) based on size-specific dose estimate (SSDE) derived using effective diameter ( Deff ) for adult chest and abdomen computed tomography (CT) procedures and to explore the feasibility of driving Deff using the product of tube current and time (mAs). In this retrospective study, dose data, scan parameters and patient body dimensions at the mid-slice level from 14 CT units (out of 63 total) were extracted. Additionally, the mAs values of the axial slice at the same z-location where the diameter measurements were made (mAs z ) were recorded. Pearson’s correlation (r) analysis was used to determine the relationship of Deff with patient BMI, weight, and mAs z . The NDRL SSDE for the chest and abdomen were 9.72 mGy and 13.4 mGy, respectively. The BMI and body weight were less correlated (r = 0.24 and r = 0.33, respectively) with Deff . The correlation between mAs z and Deff was considerably strong (r = 0.78) and can be used to predict Deff accurately. The absolute dose differences between SSDEs calculated using the AAPM–204 method and mAs z was less than 1.1 mGy (15%). Therefore, mAs z is an efficient parameter to derive Deff . Further, the direct conversion factors to estimate SSDEs at different locations along the z-direction in the scan region from corresponding mAs and CTDI vol were calculated. The NDRL SSDE suggested in the present study can be used as a reference for size-dependent dose optimisation in Sri Lanka, and existing NDRL based on CTDI vol underestimate the average adult CT dose by 36.0% and 39.7% for chest and abdomen regions respectively. The results show that using mAs z to determine SSDE is a simple and practical approach with an accuracy of 95% and 85% for abdomen and chest scans, respectively. However, the obtained linear relationship between Deff and mAs is highly dependent on the ATCM technique and the user-determined noise levels of the scanning protocol. Finally, the phantom study resulted in the strongest correlation (r = 0.99) between the D wz and mAs z , and the prediction of patient size would be more precise than Deff method.
The role of surveillance and salvage esophagectomy in previously treated esophageal cancer

Esophageal cancer remains a significant cause of cancer‐related mortality among men and women in the United States. The utility of surgery, as either an immediate or delayed resection in the form of esophagectomy following neoadjuvant therapy in local‐regionally advanced esophageal cancer, remains controversial. While neoadjuvant therapy followed by immediate surgery is a guideline‐concordant treatment, emerging data suggests that active surveillance with delayed resection at the time of local‐regional recurrence may be considered.
Pancreatic Hormone Insulin Modulates Organic Anion Transporter 1 in the Kidney: Regulation via Remote Sensing and Signaling Network

Organic anion transporter 1 (OAT1) expressed in the kidney plays an important role in the elimination of numerous anionic drugs used in the clinic. We report here that insulin, a pancreas-secreted hormone, regulated the expression and activity of kidney-specific OAT1 both in cultured cells and in rats. We showed that treatment of OAT1-expressing cells with insulin led to an increase in OAT1 expression, transport activity, and SUMOylation. Such insulin-induced increase was blocked by afuresertib, a specific inhibitor for protein kinase B (PKB), suggesting insulin regulates OAT1 through PKB signaling pathway. Furthermore, insulin stimulated transport activity and SUMOylation of endogenously expressed OAT1 in rat kidneys. In conclusion, our data support a remote sensing and signaling model, in which OAT1 plays an essential role in intercellular and inter-organ communication and in maintaining local and whole-body homeostasis. Such complex and dedicated communication is carried out by insulin, and PKB signaling and membrane sorting. Graphical Abstract
Epitaxial integration of ferromagnetic correlated oxide LaCoO3 with Si (100)

We have grown epitaxial strained LaCoO3 on (100)-oriented silicon by molecular beam epitaxy using a relaxed epitaxial SrTiO3 buffer layer. Superconducting quantum interference device magnetization measurements show that, unlike the bulk material, the ground state of the strained LaCoO3 on silicon is ferromagnetic with a TC of 85 K. First principles calculations suggest that a ferromagnetic ground state can be stabilized in LaCoO3 by a sufficiently large biaxial tensile strain with the transition accompanied by a partial untilting of the CoO6 octahedra.
Hydrovoltaic Nanogenerators for Self-Powered Sweat Electrolyte Analysis.

Human sweat comprises various electrolytes that are health status indicators. Conventional potentiometric electrolyte sensors require an electrical power source, which is expensive, bulky, and requires a complex architecture. Herein, this work demonstrates an electric nanogenerator fabricated using silicon nanowire (SiNW) arrays comprising modified carbon nanoparticles. The SiNW arrays platform is demonstrated as an effective self-powered sensor for sweat electrolyte analysis. It has been shown that an evaporation-induced water flow in nanochannels can yield an open-circuit voltage (Voc ) of 0.45 V and a short-circuit current of 10.2 µA at room temperature as a result of overlapped electric double layers. The electrolyte in the water flow results in a Voc decrease due to the charge shielding effect. The Voc is inversely proportional to the electrolyte concentration. The fabricated hydrovoltaic device shows the capability for sensing electrolytes in human sweat, which is useful in evaluating the hydration status of volunteers following intense physical exercise. The device depicts a novel response mechanism compared to conventional electrochemical sensors. Furthermore, the hydrovoltaic device shows a maximum output power of 1.42 µW, and as such has been successfully shown to drive various electronic devices including light-emitting diodes, a calculator, and an electronic timer.
Dynamical evolution of gaseous disks in halo potentials. I - Massless rings in static, spheroidal halos

We have conducted an experimental study of gaseous galaxy disks that evolve under the influence of an external halo potential. Because our numerical experiments are the first to employ a fully three-dimensional, Eulerian, hydrodynamical computer code, we have chosen the simplest possible initial conditions: the disks are massless and the external potential is either oblate or prolate spheroidal and nontumbling. The outcome and the details of each model's evolution depend critically on the degree of distortion of the halo from spherical symmetry and on the initial inclination of the disk from the equatorial plane of the halo
Oxygen vacancy-engineered titanium-based perovskite for boosting H2O activation and lower-temperature hydrolysis of organic sulfur

Significance Lower-temperature organic sulfur (COS and CS2) hydrolysis is very critical to achieve high sulfur recovery efficiency and ultra-low emissions of the Claus process. However, hydrolysis activity at low temperature may be limited by inefficient activation of H2O molecule. In this work, we revealed that a facile oxygen vacancy (VO) engineering on titanium-based perovskite allowed to boosting H2O activation and enables efficient COS and CS2 hydrolysis at 225 °C, which attained to a favorable temperature for the Claus conversion. The in-depth understanding of the very nature for the promotion role of VO in H2O molecule activation and the correlation to catalytic activity can benefit the design of efficacious catalysts for H2O-involved chemical reactions.
The Origins and Risk Factors for Serotype-2 Vaccine-Derived Poliovirus Emergences in Africa During 2016–2019

Abstract Serotype 2 oral poliovirus vaccine (OPV2) can revert to regain wild-type neurovirulence and spread to cause emergences of vaccine-derived poliovirus (VDPV2). After its global withdrawal from routine immunization in 2016, outbreak response use has created a cycle of VDPV2 emergences that threaten eradication. We implemented a hierarchical model based on VP1 region genetic divergence, time, and location to attribute emergences to campaigns and identify risk factors. We found that a 10 percentage point increase in population immunity in children younger than 5 years at the campaign time and location corresponds to a 18.0% decrease (95% credible interval [CrI], 6.3%–28%) in per-campaign relative risk, and that campaign size is associated with emergence risk (relative risk scaling with population size to a power of 0.80; 95% CrI, .50–1.10). Our results imply how Sabin OPV2 can be used alongside the genetically stable but supply-limited novel OPV2 (listed for emergency use in November 2020) to minimize emergence risk.