Miracle-dz/UniFAR-FTUs huggingface dataset:
In vitro inhibition of avian pathogenic Enterococcus cecorum isolates by probiotic Bacillus strains

ABSTRACT Enterococcus cecorum is a commensal bacteria and opportunistic pathogen that can cause outbreaks of Enterococcal spondylitis (“kinky back”) in poultry, with a growing concern worldwide. Numerous Bacillus-based probiotic strains are commercially available with proven effects in supporting gut health and growth performance, but efficacy against pathogenic E. cecorum is unknown. This study compared the in vitro inhibitory potential of cell-free supernatants (CFSs) of 18 Bacillus strains (14 commercial probiotic strains, 1 internal negative control and 3 type strains) on the growth of 9 clinical E. cecorum isolates. Standardized biomass cultures of live Bacillus were harvested and filtered to obtain CFSs. Inhibitory potential against E. cecorum isolates was assessed via a microdilution assay in which the final pathogen concentration was ∼ 104 CFU/mL. Absorbance (OD) was measured every 15 min for 15 h and used to calculate percentage growth inhibition at an OD equivalent to 0.4 in the positive control (PC) (pathogen but no CFS), and growth delay vs. PC. Growth kinetic responses of pathogen isolate-Bacillus strain combinations ranged from total pathogen inhibition to partial inhibition, lag in growth, no effect, or increased growth vs. PC. Percentage inhibition of individual isolates varied markedly among Bacillus strains, from 100% to −100% (growth promotion as recorded for the type strain) (B. amyloliquefaciens DSM7T). Five B. amyloliquefaciens CFSs produced higher average inhibition rates (>75%) than 2 out of 3 Bacillus licheniformis CFSs (−2.5, and −8.39% vs. PC, respectively) and 1 out of 2 Bacillus subtilis CFSs (7.3% vs. PC) (P < 0.05). Commercial strain 3AP4 exhibited the highest average percentage inhibition vs. PC (85.0% ± 7.9) and the most consistent inhibitory effect across pathogen isolates. The findings indicate that some commercially available poultry probiotic Bacillus strains are effective at inhibiting pathogenic E. cecorum in vitro, but effects are highly strain and pathogen isolate-dependent. Further work is required to confirm effects in vivo and isolate the inhibitory substances.
Oxidative Stress and Nutraceuticals in the Modulation of the Immune Function: Current Knowledge in Animals of Veterinary Interest

In the veterinary sector, many papers deal with the relationships between inflammation and oxidative stress. However, few studies investigate the mechanisms of action of oxidised molecules in the regulation of immune cells. Thus, authors often assume that these events, sometime leading to oxidative stress, are conserved among species. The aim of this review is to draw the state-of-the-art of the current knowledge about the role of oxidised molecules and dietary antioxidant compounds in the regulation of the immune cell functions and suggest some perspectives for future investigations in animals of veterinary interest.
Evaluation of Tumor Blood Flow Using Alternate Ascending/Descending Directional Navigation in Primary Brain Tumors: A Comparison Study with Dynamic Susceptibility Contrast Magnetic Resonance Imaging

Objective Alternate ascending/descending directional navigation (ALADDIN) is a novel arterial spin labeling technique that does not require a separate spin preparation pulse. We sought to compare the normalized cerebral blood flow (nCBF) values obtained by ALADDIN and dynamic susceptibility contrast (DSC) perfusion magnetic resonance imaging (MRI) in patients with primary brain tumors. Materials and Methods Sixteen patients with primary brain tumors underwent MRI scans including contrast-enhanced T1-weighted imaging, DSC perfusion MRI, and ALADDIN. The nCBF values of normal gray matter (GM) and tumor areas were measured by both DSC perfusion MRI and ALADDIN, which were compared by the Wilcoxon signed rank test. Subgroup analyses according to pathology were performed with the Wilcoxon signed rank test. Results Higher mean nCBF values of GM regions in the bilateral frontal lobe, temporal lobe, and caudate were detected by ALADDIN than by DSC perfusion MRI (p <0.05). In terms of the mean or median nCBF values and the mean of the top 10% nCBF values from tumors, DSC perfusion MRI and ALADDIN did not statistically significantly differ either overall or in each tumor group. Conclusion ALADDIN tended to detect higher nCBF values in normal GM, as well as higher perfusion portions of primary brain tumors, than did DSC perfusion MRI. We believe that the high perfusion signal on ALADDIN can be beneficial in lesion detection and characterization.
Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism

Recognizing substructures and their relations embedded in a molecular structure representation is a key process for structure-activity or structure-property relationship (SAR/SPR) studies. A molecular structure can be explicitly represented as either a connection table (CT) or linear notation, such as SMILES, which is a language describing the connectivity of atoms in the molecular structure. Conventional SAR/SPR approaches rely on partitioning the CT into a set of predefined substructures as structural descriptors. In this work, we propose a new method to identifying SAR/SPR through linear notation (for example, SMILES) syntax analysis with self-attention mechanism, an interpretable deep learning architecture. The method has been evaluated by predicting chemical properties, toxicology, and bioactivity from experimental data sets. Our results demonstrate that the method yields superior performance compared with state-of-the-art models. Moreover, the method can produce chemically interpretable results, which can be used for a chemist to design and synthesize the activity- or property-improved compounds.
Risk factors for vascular catheter-related bloodstream infections in pediatric intensive care units

Objectives To determine the risk factors for acquiring central line-associated blood stream infections (CLABSI) in pediatric intensive care units and to investigate the incidence and etiology of CLABSI in pediatric intensive care units with different profiles. Methods The study was a prospective cohort study in three hospitals. One of the hospitals is a large metropolitan public hospital with two pediatric intensive care units and a total of nineteen pediatric intensive care unit beds, another is a regional hospital with eight pediatric intensive care unit beds, and the third is a private hospital with fifteen beds. Patients between the ages of 1 month old and 18 years old who used a central venous catheter for over 24 hours were included. We recorded patients’ daily progress. General patient and catheter-related data were collected and used as variables. All the data were analyzed using Statistical Package for Social Science (SPSS), version 13.0, to compare patients with CLABSI with or without risk factors. Results A total of 728 patients were admitted to the pediatric intensive care units, and 170 had a central line in place for at least 24 hours. The median age was 32 months, and 97 (57%) of the patients were males. The CLABSI incidence rate was 3.9/1000 central venous catheter-days. The incidence among hospitals varied from 1.6 to 6.6. The overall mortality rate was 11.1%, and the CLABSI and non-CLABSI mortality rates were 12.9% and 10.7%, respectively. In multivariate analysis, independent risk factors for CLABSI were a longer duration of central venous catheter use (OR: 1.07; 95%CI 1.00 - 1.14; p = 0.019) and the use of more than one central venous catheter at once (OR: 2.59; 95%CI 1.17 - 5.73; p = 0.048). Conclusion A longer duration of central venous catheter use and the use of more than one central venous catheter at once were the main risk factors for CLABSI in pediatric intensive care units.
Intestinal Microbiota as a Host Defense Mechanism to Infectious Threats

The intestinal microbiota is a complex microbial community, with diverse and stable populations hosted by the gastrointestinal tract since birth. This ecosystem holds multiple anti-infectious, anti-inflammatory, and immune modulating roles decisive for intestinal homeostasis. Among these, colonization resistance refers to the dynamic antagonistic interactions between commensals and pathogenic flora. Hence, gut bacteria compete for the same intestinal niches and substrates, while also releasing antimicrobial substances such as bacteriocines and changing the environmental conditions. Short chain fatty acids (SCFAs) generated in anaerobic conditions prompt epigenetic regulatory mechanisms that favor a tolerogenic immune response. In addition, the commensal flora is involved in the synthesis of bactericidal products, namely secondary biliary acids or antimicrobial peptides (AMPs) such as cathellicidin-LL37, an immunomodulatory, antimicrobial, and wound healing peptide. Gut microbiota is protected through symbiotic relations with the hosting organism and by quorum sensing, a specific cell-to-cell communication system. Any alterations of these relationships favor the uncontrollable multiplication of the resident pathobionts or external entero-pathogens, prompting systemic translocations, inflammatory reactions, or exacerbations of bacterial virulence mechanisms (T6SS, T3SS) and ultimately lead to gastrointestinal or systemic infections. The article describes the metabolic and immunological mechanisms through which the intestinal microbiota is both an ally of the organism against enteric pathogens and an enemy that favors the development of infections.
Potential Novel Prediction of TMJ-OA: MiR-140-5p Regulates Inflammation Through Smad/TGF-β Signaling

Temporomandibular joint osteoarthritis (TMJ-OA), mainly exhibit extracellular matrix loss and condylar cartilage degradation, is the most common chronic and degenerative maxillofacial osteoarthritis; however, no efficient therapy for TMJ-OA exists due to the poor understanding of its pathological progression. MicroRNA (miR)-140-5p is a novel non-coding microRNAs (miRNAs) that expressed in osteoarthritis specifically. To investigate the molecular mechanisms of miR-140-5p in TMJ-OA, primary mandibular condylar chondrocytes (MCCs) from C57BL/6N mice were treated with interleukins (IL)-1β or transfected with miR-140-5p mimics or inhibitors, respectively. The expression of matrix metallopeptidase (MMP)-13, miR-140-5p, nuclear factor (NF)-kB, Smad3 and transforming growth factor (TGF)-β3 were examined by western blotting or quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The interaction between the potential binding sequence of miR-140-5p and the 3′-untranslated region (3′UTR) of Smad3 mRNA was testified by dual-luciferase assay. Small Interfering RNA of Smad3 (Si-Smad3) was utilized to further identify the role of Smad3 mediated by miR-140-5p. The data showed MMP13, miR-140-5p and NF-kB increased significantly in response to IL-1β inflammatory response in MCCs, meanwhile, Smad3 and TGF-β3 reduced markedly. Moreover, transfection of miR-140-5p mimics significantly suppressed the expression of Smad3 and TGF-β3 in MCCs, while miR-140-5p inhibitors acted in a converse manner. As the luciferase reporter of Smad3 mRNA observed active interaction with miR-140-5p, Smad3 was identified as a direct target of miR-140-5p. Additionally, the expression of TGF-β3 was regulated upon the activation of Smad3. Together, these data suggested that miR-140-5p may play a role in regulating mandibular condylar cartilage homeostasis and potentially serve as a novel prognostic factor of TMJ-OA-like pathology.
Outcome Following the Treatment of Ventriculitis Caused by Multi/Extensive Drug Resistance Gram Negative Bacilli; Acinetobacter baumannii and Klebsiella pneumonia

Introduction: CNS ventriculitis is a serious complication following an intracranial insult that demands immediate treatment with broad-spectrum antibiotics in a critical care setting. Infections due to multi/extensive drug resistance (MDR/XDR) microorganisms are very challenging, which may demand an additional approach to the ongoing practice; intravenous and intraventricular administration of antibiotics. Aim: To study the efficacy and safety of thorough ventricular irrigation followed by daily intraventricular antibiotic administration in patients with MDR/XDR ventriculitis. Materials and Methods: A retrospective analysis was done on 19 inpatients with ventriculitis caused by Acinetobacter baumannii (AB) or Klebsiella pneumonia (KP), at Shanghai Tenth People's Hospital from January 2016 to October 2017. We reviewed our experience; the role of thorough ventricular irrigation with Colistin mixed normal saline, followed by intraventricular Colistin therapy. Treatment outcomes were evaluated based on the clinical symptoms, Cerebro-Spinal Fluid (CSF) culture, laboratory findings and complications. Results: A total of 19 patients were included (15 males and 4 females), with a mean age in years of 51, which ranged from 18–67. Fourteen patients had Acinetobacter baumannii (AB) and 5 had Klebsiella pneumoniae (KP). The average CSF sterilization period following ventricular irrigation and intraventricular Colistin was 6 days. Sixteen patients (84%) were cured, and 3 patients (15%) died during the course of the treatment. Conclusion: In addition to Intraventricular Colistin, thorough ventricular irrigation could increase the cure rate up to 84% in patients suffering from MDR/XDR CNS ventriculitis.
The ABC Guide to Fluorescent Toolsets for the Development of Future Biomaterials

In recent decades, diversified approaches using nanoparticles or nano-structured scaffolds have been applied to drug delivery and tissue engineering. Thanks to recent interdisciplinary studies, the materials developed have been intensively evaluated at animal level. Despite these efforts, less attention has been paid to what is really going on at the subcellular level during the interaction between a nanomaterial and a cell. As the proposed concept becomes more complex, the need for investigation of the dynamics of these materials at the cellular level becomes more prominent. For a deeper understanding of cellular events, fluorescent imaging techniques have been a powerful means whereby spatiotemporal information related to cellular events can be visualized as detectable fluorescent signals. To date, several excellent review papers have summarized the use of fluorescent imaging toolsets in cellular biology. However, applying these toolsets becomes a laborious process for those who are not familiar with imaging studies to engage with owing to the skills gap between them and cell biologists. This review aims to highlight the valuable essentials of fluorescent imaging as a tool for the development of effective biomaterials by introducing some cases including photothermal and photodynamic therapies. This distilled information will be a convenient short-cut for those who are keen to fabricate next generation biomaterials.
An Improved A* Algorithm Based on Hesitant Fuzzy Set Theory for Multi-Criteria Arctic Route Planning

This paper presents a new route planning system for the purpose of evaluating the strategic prospects for future Arctic routes. The route planning problem can be regarded as a multi criteria decision making problem with large uncertainties originating from multi-climate models and experts’ knowledge and can be solved by a modified A* algorithm where the hesitant fuzzy set theory is incorporated. Compared to the traditional A* algorithm, the navigability of the Arctic route is firstly analyzed as a measure to determine the obstacle nodes and three key factors to the vessel navigation including sailing time, economic cost and risk are overall considered in the HFS-A* algorithm. A numerical experiment is presented to test the performance of the proposed algorithm.
Intelligent Dynamic Backlash Agent: A Trading Strategy Based on the Directional Change Framework

The Directional Changes (DC) framework is an approach to summarize price movement in financial time series. Some studies have tried to develop trading strategies based on the DC framework. Dynamic Backlash Agent (DBA) is a trading strategy that has been developed based on the DC framework. Despite the promising results of DBA, DBA employed neither an order size management nor risk management components. In this paper, we present an improved version of DBA named Intelligent DBA (IDBA). IDBA overcomes the weaknesses of DBA as it embraces an original order size management and risk management modules. We examine the performance of IDBA in the forex market. The results suggest that IDBA can provide significantly greater returns than DBA. The results also show that the IDBA outperforms another DC-based trading strategy and that it can generate annualized returns of about 30% after deducting the bid and ask spread (but not the transaction costs).
Subcomplete forcing principles and definable well‐orders

It is shown that the boldface maximality principle for subcomplete forcing, MPSC(Hω2) , together with the assumption that the universe has only set many grounds, implies the existence of a well‐ordering of ℘(ω1) definable without parameters. The same conclusion follows from MPSC(Hω2) , assuming there is no inner model with an inaccessible limit of measurable cardinals. Similarly, the bounded subcomplete forcing axiom, together with the assumption that x# does not exist, for some x⊆ω , implies the existence of a well‐ordering of ℘(ω1) which is Δ1‐definable without parameters, and Δ1(Hω2) ‐definable using a subset of ω1 as a parameter. This well‐order is in L(℘(ω1)) . Enhanced versions of bounded forcing axioms are introduced that are strong enough to have the implications of MPSC(Hω2) mentioned above, and along the way, a bounded forcing axiom for countably closed forcing is proposed.
On the Use of Learnheuristics in Vehicle Routing Optimization Problems with Dynamic Inputs

Freight transportation is becoming an increasingly critical activity for enterprises in a global world. Moreover, the distribution activities have a non-negligible impact on the environment, as well as on the citizens’ welfare. The classical vehicle routing problem (VRP) aims at designing routes that minimize the cost of serving customers using a given set of capacitated vehicles. Some VRP variants consider traveling times, either in the objective function (e.g., including the goal of minimizing total traveling time or designing balanced routes) or as constraints (e.g., the setting of time windows or a maximum time per route). Typically, the traveling time between two customers or between one customer and the depot is assumed to be both known in advance and static. However, in real life, there are plenty of factors (predictable or not) that may affect these traveling times, e.g., traffic jams, accidents, road works, or even the weather. In this work, we analyze the VRP with dynamic traveling times. Our work assumes not only that these inputs are dynamic in nature, but also that they are a function of the structure of the emerging routing plan. In other words, these traveling times need to be dynamically re-evaluated as the solution is being constructed. In order to solve this dynamic optimization problem, a learnheuristic-based approach is proposed. Our approach integrates statistical learning techniques within a metaheuristic framework. A number of computational experiments are carried out in order to illustrate our approach and discuss its effectiveness.
Differential-Evolution-Based Coevolution Ant Colony Optimization Algorithm for Bayesian Network Structure Learning

Learning the Bayesian networks (BNs) structure from data has received increasing attention. Many heuristic algorithms have been introduced to search for the optimal network that best matches the given training data set. To further improve the performance of ant colony optimization (ACO) in learning the BNs structure, this paper proposes a new improved coevolution ACO (coACO) algorithm, which uses the pheromone information as the cooperative factor and the differential evolution (DE) as the cooperative strategy. Different from the basic ACO, the coACO divides the entire ant colony into various sub-colonies (groups), among which DE operators are adopted to implement the cooperative evolutionary process. Experimental results demonstrate that the proposed coACO outperforms the basic ACO in learning the BN structure in terms of convergence and accuracy.
Developing a Business Plan for a Library Publishing Program

Over the last twenty years, library publishing has emerged in higher education as a new class of publisher. Conceived as a response to commercial publishing practices that have strained library budgets and prevented scholars from openly licensing and sharing their works, library publishing is both a local service program and a broader movement to disrupt the current scholarly publishing arena. It is growing both in numbers of publishers and numbers of works produced. The commercial publishing framework which determines the viability of monetizing a product is not necessarily applicable for library publishers who exist as a common good to address the needs of their academic communities. Like any business venture, however, library publishers must develop a clear service model and business plan in order to create shared expectations for funding streams, quality markers, as well as technical and staff capacity. As the field is maturing from experimental projects to full programs, library publishers are formalizing their offerings and limitations. The anatomy of a library publishing business plan is presented and includes the principles of the program, scope of services, and staffing requirements. Other aspects include production policies, financial structures, and measures of success.
Parallel Reservoir Simulation with OpenACC and Domain Decomposition

Parallel reservoir simulation is an important approach to solving real-time reservoir management problems. Recently, there is a new trend of using a graphics processing unit (GPU) to parallelize the reservoir simulations. Current GPU-aided reservoir simulations focus on compute unified device architecture (CUDA). Nevertheless, CUDA is not functionally portable across devices and incurs high amount of code. Meanwhile, domain decomposition is not well used for GPU-based reservoir simulations. In order to address the problems, we propose a parallel method with OpenACC to accelerate serial code and reduce the time and effort during porting an application to GPU. Furthermore, the GPU-aided domain decomposition is developed to accelerate the efficiency of reservoir simulation. The experimental results indicate that (1) the proposed GPU-aided approach can outperform the CPU-based one up to about two times, meanwhile with the help of OpenACC, the workload of the transplant code was reduced significantly by about 22 percent of the source code, (2) the domain decomposition method can further improve the execution efficiency up to 1.7×. The proposed parallel reservoir simulation method is a efficient tool to accelerate reservoir simulation.