Miracle-dz/UniFAR-FTUs huggingface dataset:
T4SP: a novel tool and database for type IV secretion systems in bacterial genomes.

Secretion systems, which can mediate the macromolecules to pass across cellular membranes, are essential for virulent and genetic material exchange among bacterial species [1] . Type IV secretion system (T4SS) is one of the secretion systems and it usually consists of 12 genes: VirB1, VirB2 …VirB11, and VirD4 [2] . The structure and molecular mechanisms of these genes have been well
MIMIC: locating and understanding bugs by analyzing mimicked executions

Automated debugging techniques aim to help developers locate and understand the cause of a failure, an extremely challenging yet fundamental task. Most state-of-the-art approaches suffer from two problems: they require a large number of passing and failing tests and report possible faulty code with no explanation. To mitigate these issues, we present MIMIC, a novel automated debugging technique that combines and extends our previous input generation and anomaly detection techniques. MIMIC (1) synthesizes multiple passing and failing executions similar to an observed failure and (2) uses these executions to detect anomalies in behavior that may explain the failure. We evaluated MIMIC on six failures of real-world programs with promising results: for five of these failures, MIMIC identified their root causes while producing a limited number of false positives. Most importantly, the anomalies identified by MIMIC provided information that may help developers understand (and ultimately eliminate) such root causes.
Qubit allocation

In May of 2016, IBM Research has made a quantum processor available in the cloud to the general public. The possibility of programming an actual quantum device has elicited much enthusiasm. Yet, quantum programming still lacks the compiler support that modern programming languages enjoy today. To use universal quantum computers like IBM's, programmers must design low-level circuits. In particular, they must map logical qubits into physical qubits that need to obey connectivity constraints. This task resembles the early days of programming, in which software was built in machine languages. In this paper, we formally introduce the qubit allocation problem and provide an exact solution to it. This optimal algorithm deals with the simple quantum machinery available today; however, it cannot scale up to the more complex architectures scheduled to appear. Thus, we also provide a heuristic solution to qubit allocation, which is faster than the current solutions already implemented to deal with this problem.
Remote monitoring of dynamic canopy photosynthesis with high time resolution light-induced fluorescence transients

Understanding the net photosynthesis of plant canopies requires quantifying photosynthesis in challenging environments, principally due to the variable light intensities and qualities generated by sunlight interactions with clouds and surrounding foliage. The dynamics of sunflecks and rates of change in light intensity at the beginning and end of sustained light (SL) events makes photosynthetic measurements difficult, especially when dealing with less accessible parts of plant foliage. High time resolved photosynthetic monitoring from pulse amplitude modulated (PAM) fluorometers has limited applicability due to the invasive nature of frequently applied saturating flashes. An alternative approach used here provides remote (<5 m), high time resolution (10 s), PAM equivalent but minimally invasive measurements of photosynthetic parameters. We assessed the efficacy of the QA flash protocol from the Light-Induced Fluorescence Transient (LIFT) technique for monitoring photosynthesis in mature outer canopy leaves of potted Persea americana Mill. cv. Haas (Avocado) trees in a semi-controlled environment and outdoors. Initially we established that LIFT measurements were leaf angle independent between ±40° from perpendicular and moreover, that estimates of 685 nm reflectance (R685) from leaves of similar chlorophyll content provide a species dependent, but reasonable proxy for incident light intensity. Photosynthetic responses during brief light events (≤10 min), and the initial stages of SL events, showed similar declines in the quantum yield of photosystem II (ΦII) with large transient increases in 'constitutive loss processes' (ΦNO) prior to dissipation of excitation by non-photochemical quenching (ΦNPQ). Our results demonstrate the capacity of LIFT to monitor photosynthesis at a distance during highly dynamic light conditions that potentially may improve models of canopy photosynthesis and estimates of plant productivity. For example, generalized additive modelling performed on the 85 dynamic light events monitored identified negative relationships between light event length and ∆ΦII and ∆electron transport rate using either ∆photosynthetically active radiation or ∆R685 as indicators of leaf irradiance.
Nanostructures and Nanotechnology: Micro- and nanofluidics

Preface 1. Introduction and overview 2. Solid state physics in a nutshell 3. Bulk materials 4. Fabrication and characterization at the nanoscale 5. Real solids: defects, interactions, confinement 6. Charge transport and nanoelectronics 7. Magnetism and magnetoelectronics 8. Photonics 9. Micro and nanomechanics 10. Micro and nanofluidics 11. Bionanotechnology: a very brief overview 12. Nanotechnology and the future Appendix: common quantum mechanics and statistical mechanics results References Index.
LC-MS based metabolic and metabonomic studies of Panax ginseng.

INTRODUCTION Panax ginseng has received much attention as a valuable health supplement with medicinal potential. Its chemical diversity and multiple pharmacological properties call for comprehensive methods to better understand the effects of ginseng and ginsenosides. Liquid chromatography-mass spectrometry (LC-MS) based metabonomic approaches just fit the purpose. OBJECTIVE Aims to give a review of recent progress on LC-MS based pharmacokinetic, metabolic, and phytochemical metabolomic studies of ginseng, and metabonomic studies of ginseng intervention effects. METHODS The review has four sections: the first section discusses metabolic studies of ginsenosides based on LC-MS, the second focuses on ginsenoside-drug interactions and pharmacokinetic interaction between herb compounds based on LC-MS, the third is phytochemical metabolomic studies of ginseng based on LC-MS, and the fourth deals with metabonomic studies of ginseng intervention effects based on LC-MS. RESULTS LC-MS based metabonomic research on ginseng include analysis of single ginsenoside and total ginsenosides. The theory of multi-components and multi-targeted mechanisms helps to explain ginseng effects. CONCLUSION LC-MS based metabonomics is a promising way to comprehensively assess ginseng. It is valuable for quality control and mechanism studies of ginseng.
Discovering Discontinuity in Big Financial Transaction Data

Business transactions are typically recorded in the company ledger. The primary purpose of such financial information is to accompany a monthly or quarterly report for executives to make sound business decisions and strategies for the next business period. These business strategies often result in transitions that cause underlying infrastructures and components to change, including alteration in the nomenclature system of the business components. As a result, a transaction stream of an affected component would be replaced by another stream with a different component name, resulting in discontinuity of a financial stream of the same component. Recently, advancement in large-scale data mining technologies has enabled a set of critical applications to utilize knowledge extracted from a vast amount of existing data that would otherwise have been unused or underutilized. In financial and services computing domains, recent studies have illustrated that historical financial data could be used to predict future revenues and profits, optimizing costs, among other potential applications. These prediction models rely on long-term availability of the historical data that traces back for multiple years. However, the discontinuity of the financial transaction stream associated with a business component has limited the learning capability of the prediction models. In this article, we propose a set of machine learning–based algorithms to automatically discover component name replacements, using information available in general ledger databases. The algorithms are designed to be scalable for handling massive data points, especially in large companies. Furthermore, the proposed algorithms are generalizable to other domains whose data is time series and shares the same nature as the financial data available in business ledgers. A case study of real-world IBM service delivery retrieved from four different geographical regions is used to validate the efficacy of the proposed methodology.
Route dynamics for Shortest Path First routing in mobile ad hoc networks

This paper investigates the route dynamics of shortest-path first (SPF) routing in mobile ad hoc networks (MANETs). In particular, we find, from a statistical analysis of route duration and route change interval, that route dynamics may require complex modelling. Our analysis considers various mobility models, node velocities and node densities of the MANET network. Our findings show that, in a MANET with moderate or high rate of mobility, the route duration could be approximated by an exponential distribution with approximate parameters, while the route duration of specific lengths could not. Our findings suggest that minimum hop-count routing in MANETs may be inappropriate and that further investigation is required in order to develop models that let us understand MANET route dynamics.
Decontamination and CJD: The Latest Guidance

Professor Don Jeffries, Chair of the Advisory Committee on Dangerous Pathogens Working Group on Transmissible Spongiform Encephalopathies (ACDP TSE), Deputy Chair of the Creutzfeldt-Jakob Disease (CJD) Incidents Panel, and Chair of the Department of Health Decontamination Research Group discusses the latest guidance on the prevention of transmissible spongiform encephalopathies (TSEs). This article is based on the presentation he gave at AfPP's Annual Congress in October 2005.
An Iterative Method for Moving Target Localization Using TDOA and FDOA Measurements

For moving targets localization, incorporating frequency-difference-of-arrival (FDOA) measurements in the commonly used time-difference-of-arrival (TDOA) positioning systems will improve performance. Such an approach still has unresolved technical challenges. The commonly used maximum likelihood estimator (MLE) is nonconvex and highly nonlinear, and the parameters to be estimated are mutually coupled in the positioning process. The goal of this paper is to develop an effective iterative method that resolves these challenges for moving target localization using TDOA and FDOA. Specifically, a semidefinite programming (SDP) method is proposed to transform the MLE problem into a convex optimization problem. To improve the performance further, we develop an iterative method that uses the position and velocity estimates obtained using the SDP method as the initial values. This iterative method includes two steps: update of the velocity by using a weighted least squares method and update of the position by using SDP. The major advantage of the proposed scheme is that it significantly outperforms existing methods at moderate to high noise levels, which is validated via extensive numerical results.
Information Spreading Forensics via Sequential Dependent Snapshots

Mining the characteristics of information spreading in networks is crucial in communication studies, network security management, epidemic investigations, etc. Previous works are restrictive because they mainly focused on the information source detection using either a single observation, or multiple but independent observations of the underlying network while assuming a homogeneous information spreading rate. We conduct a theoretical and experimental study on information spreading, and propose a new and novel estimation framework to estimate 1) information spreading rates, 2) start time of the information source, and 3) the location of information source by utilizing multiple sequential and dependent snapshots where information can spread at heterogeneous rates. Our framework generalizes the current state-of-the-art rumor centrality [1] and the union rumor centrality [2]. Furthermore, we allow heterogeneous information spreading rates at different branches of a network. Our framework provides conditional maximum likelihood estimators for the above three metrics and is more accurate than rumor centrality and Jordan center in both synthetic networks and real-world networks. Applying our framework to the Twitter’s retweet networks, we can accurately determine who made the initial tweet and at what time the tweet was sent. Furthermore, we also validate that the rates of information spreading are indeed heterogeneous among different parts of a retweet network.
Catheter-based renal sympathetic denervation: limitations to and gaps in the evidence

Purpose of review Renal sympathetic nerves play a significant role in the development and maintenance of hypertension. Percutaneous catheter-based radioablation of the sympathetic nerves around the renal arteries is a true innovation in follow up to prior animal studies. In this opinion article, we will review the role of the renal sympathetic network in hypertension, and the evidence (or the lack of it) for renal sympathetic denervation as a treatment modality for human hypertension. Recent findings Over the last 5 years, path-breaking research has raised the promise of a dramatically effective therapy for treatment of resistant hypertension in the form of renal sympathetic denervation. Unfortunately, on the basis of limited proof-of-concept and prospective observational studies, this method was widely perceived as a proven therapy for resistant hypertension. As we have learnt from history, only properly designed prospective randomized controlled trials can tell whether that is indeed the truth. Summary Catheter-based renal sympathetic denervation, despite the recent setbacks, remains a novel and innovative therapeutic intervention, which may still have a role to play in the treatment of carefully selected patients with truly resistant hypertension. Mechanistic studies designed to address the cause of the blood pressure response (or lack thereof) to renal denervation are the next logical step. However, the long-term implications of renal denervation, especially safety issues with respect to the lack of renal sympathetic response in times of physiological need, are not well understood.
Vision-inertia based navigation algorithms for quadrotors

In this paper, the navigation problem is investigated for quadrotors which fly in a GPS-denied indoor environment with ground grids. A vision-inertia based navigation algorithm is proposed which only uses the information of the grid intersection points and inertial measurement unit. First, the grid lines are detected by merging pixels with adjacent location and approximate intensity. Characteristic parameters of the lines are obtained by solving a least square problem. Then, the locations of the intersection points are calculated using these characteristic parameters. Secondly, the intersection points are matched with the corresponding points located in the real environment by solving a joint optimization problem, meanwhile the optimal homography matrix is obtained. Thirdly, the navigation information is estimated by an Extended Kalman Filter which uses the pose recovered from the homography matrix as measurements. Finally, the experiment results show the effectiveness of the proposed navigation method.
Cortical Visual Connections via the Corpus Callosum are Asymmetrical in Human Infantile Esotropia

ABSTRACT Purpose: Besides chiasmal hemidecussation, interhemispheric connections are likely important in human binocularity. The corpus callosum (CC) is the major fiber bundle in the mammalian brain which mostly connects homologous cortical areas in the two hemispheres. Visual interhemispheric connections were found abnormal in strabismic cats. No studies have investigated these pathways in humans with infantile strabismus. Methods: Diffusion tensor imaging was used in four subjects with infantile esotropia (IE) and nine control subjects with normal binocularity, in order to study interhemispheric fibers in the CC connecting the right and left primary visual cortical areas. Results: The number of callosal fibers linking both visual cortical areas between the hemispheres was found to be higher in subjects with IE. Also in IE, the amount of visual callosal fibers found after analysis from the primary visual cortical areas on one side appeared significantly different from the amount starting from the contralateral primary visual areas. The distribution area on one side is wider. Conclusion: We show callosal visual fibers to be abnormal in human IE. Subjects with IE showed abnormal numbers of transcallosal fibers connecting the visual cortical areas on both sides which likely results from an abnormal elimination process during development. Pruning of these fibers in IE favors the side of the visual cortex ipsilateral to the dominant eye. This study underlines the likely role of the CC in the development of human binocularity.
In vitro fibroblast migration by sustained release of PDGF-BB loaded in chitosan nanoparticles incorporated in electrospun nanofibers for wound dressing applications

Abstract Migration of fibroblasts into wound area is a critical phenomenon in wound healing process. We used an appropriate system to fabricate an electrospun bioactive scaffold with controlled release of PDGF-BB in order to induce migration of primary skin fibroblast cells. First of all, protein-loaded chitosan nanoparticles based on ionic gelation interaction between chitosan and sodium tripolyphosphate were prepared. Then polycaprolactone electrospun fibers containing chitosan nanoparticles or PDGF-BB-loaded chitosan nanoparticles were prepared. Cellular attachment and morphology of cells seeded on scaffolds with or without PDGF-BB were evaluated by using a fluorescence microscope and scanning electron microscopy. Cells were well-oriented 72 h after seeding on the scaffolds containing PDGF-BB. The mean aspect ratio of populations on scaffold containing PDGF-BB-loaded chitosan nanoparticles was significantly greater than those on the scaffold containing chitosan nanoparticles but no PDGF-BB. Furthermore, the Arp2 gene, which is involved in cell protrusion formation, showed about three times more expression at mRNA level, in cells seeding on PDGF-BB-containing scaffold compared to cells seeding on scaffold containing only chitosan nanoparticles, using Real Time PCR test. Finally, under agarose migration assay results demonstrated that cells’ chemotaxic behavior was more toward scaffold containing PDGF-BB compared to the PDGF-BB alone or FBS group. In addition, in terms of distance, the cell mass could grow faster, in response to scaffold containing PDGF-BB compared to FBS or PDGF-BB alone; however, the number of migrating cells might be the same or significantly higher in the latter groups.
Characterization of cellular and matrix alterations in the early pathogenesis of osteochondritis dissecans in pigs using second harmonic generation and two‐photon excitation fluorescence microscopy

Osteochondritis dissecans is a joint disease that is observed in several species. The disease can develop as a cause of ischemic chondronecrosis in the epiphyseal growth cartilage. Some lesions of chondronecrosis undergo spontaneous resolution, but it is not possible to predict whether a lesion will resolve or progress and require intervention. Proliferation of cells into clusters occurs at the lesion margin, but it is unclear if the clusters have a repair function. The aims of the current study were to examine clusters and potential matrix changes in response to ischemic chondronecrosis in the distal femur of 10 pigs aged 70–180 days using advanced microscopy based on two‐photon excitation fluorescence and second harmonic generation. These microscopy techniques can perform 3D imaging of cells and collagen without staining. The results indicated a lower collagen density in the chondronecrotic areas compared to the normal growth cartilage, and fissures and breaks in the matrix integrity were demonstrated that potentially can propagate and cause osteochondritis dissecans. A higher number of cells in clusters was correlated with reduction in collagen density in the lesions. Some of the cells in the clusters had a morphology similar to progenitor cells, suggesting a potential repair role of the clusters. The study has shed further light on the secondary responses after initial lesion formation, which information can be of potential use to create models that can predict lesion progression and that may hence avoid unnecessary interventions in the future. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2089–2098, 2018.
Crack Extension Resistance of Post-Fire Concrete

Wedge-splitting test is carried out in present research.Determination of the residual crack extension resistance curves (KR-curves) associated with cohesive force distribution on fictitious crack zone of complete fracture process is implemented. In each temperature, with the distribution of cohesive force along the fracture process zone, the residual fracture toughness KR (Δ̱) increases with increasing crack length Δ̱. Whereas the KR-curves decrease with increasing temperatures Tm for the thermal damage induced.
Dynamic Compensation Technique for POF Curvature Sensors

Polymer optical fibers (POF) can be applied as curvature sensors due to its high strain limits, fracture toughness, and flexibility in bend. However, POFs present viscoelastic behavior, which leads to a phase lag between the stress and strain. The polymer viscoelasticity can be associated to the high hysteresis and the errors that curvature sensors based on POF may present. For this reason, this paper proposes a dynamic compensation technique based on the angular velocity of the sensor. The technique comprises of initial quasi-static tests and tests with different angular velocities for the reduction of the sensor root mean squared error (RMSE) and hysteresis. Results show a reduction of both hysteresis and RMSE in almost all angular velocities tested. The mean reduction of the hysteresis is 20%. Whereas a mean reduction of about 3 times of the RMSE was obtained. Furthermore, the compensation technique results on a calibration equation, which can be applied in real-time measurements.