Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA

Abstract Aphanomyces astaci causes crayfish plague, which is a devastating disease of European freshwater crayfish. The likely first introduction of A. astaci into Europe was in the mid-19th century in Italy, presumably with the introduction of North American crayfish. These crayfish can carry A. astaci in their cuticle as a benign infection. Aphanomyces astaci rapidly spread across Europe causing the decline of the highly susceptible indigenous crayfish species. Random amplified polymorphic DNA-PCR analysis of A. astaci pure cultures characterized five genotype groups (A, B, C, D and E). Current A. astaci genotyping techniques (microsatellites and genotype-specific regions, both targeting nuclear DNA) can be applied directly to DNA extracted from infected cuticles but require high infection levels. Therefore, they are not suitable for genotyping benign infections in North American crayfish (carriers). In the present study, we combine bioinformatics and molecular biology techniques to develop A. astaci genotyping molecular markers that target the mitochondrial DNA, increasing the sensitivity of the genotyping tools. The assays were validated on DNA extracts of A. astaci pure cultures, crayfish tissue extractions from crayfish plague outbreaks and tissue extractions from North American carriers. We demonstrate the presence of A. astaci genotype groups A and B in UK waters.
Grand Challenges of Perovskite and Metal Oxide-based Membrane: A Form of Dual-layer Hollow Fibre

Perovskite and metal oxides-based dual-layer hollow fibre membrane (DHF) has a high appeal as separator and catalyst for methane conversion application which operated at intermediate and high temperature. The membrane mostly fabricated via the co-extrusion followed by co-sintering method, which is quite challenging, due to the complexity to handle the barrier between layers from delamination, membrane cracking and crystal structure distortion which affects the material performance in a DHF form. This recent review clarifies the challenges in the DHF fabrication process to regulate physical and chemical properties in terms of mechanical strength, tightness, elemental distribution, and crystal structure stability. The based material of the membrane focuses on NiO-YSZ in the inner layer directly interconnected with LSCF-YSZ in the outer layer. The understanding of the challenges in DHF fabrication, will further reduce crucial errors in the fabrication process and accelerate performance improvement for application such as syngas, methanol and long-chain hydrocarbons production, and solid oxide fuel cell.
Assessing noninferiority: Evaluating efficacy of a new treatment without complete data

The FDA released the final guidance on noninferiority trials in November 2016. In noninferiority trials, validity of the assessment of the efficacy of the test treatment depends on the control treatment's efficacy. Therefore, it is critically important that there be a reliable estimate of the control treatment effect—which is generally obtained from historical trials, and often assumed to hold in the current setting (the assay constancy assumption). Validating the constancy assumption requires clinical data, which are typically lacking. The guidance acknowledges that “lack of constancy can occur for many reasons. ” We clarify the objectives of noninferiority trials. We conclude that correction for bias, rather than assay constancy, is critical to conducting valid noninferiority trials. We propose that assay constancy not be assumed and discounting or thresholds be used to address concern about loss of historical efficacy. Examples are provided for illustration.
Electrophoretic Separation on an Origami Paper-Based Analytical Device Using a Portable Power Bank

The electrophoresis of ampholytes such as amino acids on a paper device is difficult because of the variation of pH distribution in time. On the basis of this observation, we propose a paper-based analytical device (PAD) with origami structure. By folding a filter paper, a low operation voltage of 5 V was achieved, where the power was supplied by a 5 V 1.5 A portable power bank through the USB type A receptacle. As a demonstration, we carried out the electrophoretic separation of pI markers (pI 5.5 and 8.7). The separation was achieved within 4 min before the pH distribution on the paper varied. Though the separation distance was small, it could be increased by expanding the origami structure. This result indicates that our proposed PAD is useful for electrophoretic separation on a paper device.
Plant Virus-Like Particle In Situ Vaccine for Intracranial Glioma Immunotherapy

Despite aggressive multi-modality treatment with surgery, radiation and chemotherapies, malignant glioma inevitably recurs and has dismal survival rates. Recent progress in immunotherapy has led to a resurgence of interest, and immunotherapies are being investigated for treatment of glioma. However, the unique brain anatomy and a highly immunosuppressive glioma microenvironment pose significant challenges to achieving efficacy. Thus, there is a critical need for assessment of next-generation immunotherapies for glioma. In this study, we have investigated the efficacy of the nanoparticle platform technology based on plant-derived Cowpea mosaic virus like particles (empty CPMV or eCPMV) to instigate a potent immune response against intracranial glioma. CPMV immunotherapy has been shown to efficiently reverse the immunosuppressive tumor microenvironments in pre-clinical murine models of dermal melanoma and metastatic melanoma, metastatic breast cancer, intraperitoneal ovarian cancer and in canine patients with oral melanoma. In the present study, we demonstrate that in situ administration of CPMV immunotherapy in the setting of glioma can effectively recruit unique subset of effector innate and adaptive immune cells to the brain parenchyma while reducing immune suppressive cellular population, leading to regression of intracranial glioma. The in situ CPMV nanoparticle vaccine offers a potent yet safe and localized immunotherapy for intracranial glioma.
Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota

Significance This study illustrates the dynamics of the oral microbiome during long-term starvation. After an initial ecological collapse, only three species were recoverable and displayed significant transcriptional activity: Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens. Klebsiella spp. are significant human pathogens and are frequently resistant to multiple classes of antibiotics. In addition to its status as a clinical scourge in its own right, K. pneumoniae has emerged as a chief facilitator in the transfer of drug resistance genes from the environment to pathogens. Hospital surfaces contaminated with oral fluids are well-documented sources of outbreaks of drug-resistant Enterobacteriaceae; therefore, the ability of Klebsiella to outcompete its neighbors during starvation and survive long-term in saliva is particularly noteworthy. It is well-understood that many bacteria have evolved to survive catastrophic events using a variety of mechanisms, which include expression of stress-response genes, quiescence, necrotrophy, and metabolic advantages obtained through mutation. However, the dynamics of individuals leveraging these abilities to gain a competitive advantage in an ecologically complex setting remain unstudied. In this study, we observed the saliva microbiome throughout the ecological perturbation of long-term starvation, allowing only the species best equipped to access and use the limited resources to survive. During the first several days, the community underwent a death phase that resulted in a ∼50–100-fold reduction in the number of viable cells. Interestingly, after this death phase, only three species, Klebsiella pneumoniae, Klebsiella oxytoca, and Providencia alcalifaciens, all members of the family Enterobacteriaceae, appeared to be transcriptionally active and recoverable. Klebsiella are significant human pathogens, frequently resistant to multiple antibiotics, and recently, ectopic colonization of the gut by oral Klebsiella was documented to induce dysbiosis and inflammation. MetaOmics analyses provided several leads for further investigation regarding the ecological success of the Enterobacteriaceae. The isolates accumulated single nucleotide polymorphisms in known growth advantage in stationary phase alleles and produced natural products closely resembling antimicrobial cyclic depsipeptides. The results presented in this study suggest that pathogenic Enterobacteriaceae persist much longer than their more benign neighbors in the salivary microbiome when faced with starvation. This is particularly significant, given that hospital surfaces contaminated with oral fluids, especially sinks and drains, are well-established sources of outbreaks of drug-resistant Enterobacteriaceae.
Novel Surface-Enhanced Raman Spectroscopy Techniques for DNA, Protein and Drug Detection

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique in which the Raman scattering signal strength of molecules, absorbed by rough metals or the surface of nanoparticles, experiences an exponential growth (103–106 times and even 1014–1015 times) because of electromagnetic or chemical enhancements. Nowadays, SERS has attracted tremendous attention in the field of analytical chemistry due to its specific advantages, including high selectivity, rich informative spectral properties, nondestructive testing, and the prominent multiplexing capabilities of Raman spectroscopy. In this review, we present the applications of state-of-the-art SERS for the detection of DNA, proteins and drugs. Moreover, we focus on highlighting the merits and mechanisms of achieving enhanced SERS signals for food safety and clinical treatment. The machine learning techniques, combined with SERS detection, are also indicated herein. This review concludes with recommendations for future studies on the development of SERS.
Draft Genome Sequence of Broad-Spectrum Antibiotic-Producing Marine Verrucosispora sp. Strain FIM060022

Verrucosispora sp. strain FIM060022 shows multiple biological activities and produces polytype structure compounds, including abyssomicins, proximicin A, lumichrome, denosine, and desferrioxamine-like compounds. ABSTRACT Verrucosispora sp. strain FIM060022 shows multiple biological activities and produces polytype structure compounds, including abyssomicins, proximicin A, lumichrome, denosine, and desferrioxamine-like compounds. We present the draft genome sequence of the strain to help predict the biosynthesis of these compounds, identify further biosynthetic potential, and facilitate directed secondary metabolite production.
A bronchial‐airway gene‐expression classifier to improve the diagnosis of lung cancer: Clinical outcomes and cost‐effectiveness analysis

Bronchoscopy is the safest procedure for lung cancer diagnosis when an invasive evaluation is required after imaging procedures. However, its sensitivity is relatively low, especially for small and peripheral lesions. We assessed benefits and costs of introducing a bronchial gene‐expression classifier (BGC) to improve the performance of bronchoscopy and the overall diagnostic process for early detection of lung cancer. We used discrete‐event simulation to compare clinical and economic outcomes of two different strategies with the standard practice in former and current smokers with indeterminate nodules: (i) location‐based strategy—integrated the BGC to the bronchoscopy indication; (ii) simplified strategy—extended use of bronchoscopy plus BGC also on small and peripheral lesions. Outcomes modeled were rate of invasive procedures, quality‐adjusted‐life‐years (QALYs), costs and incremental cost‐effectiveness ratios. Compared to the standard practice, the location‐based strategy (i) reduced absolute rate of invasive procedures by 3.3% without increasing costs at the current BGC market price. It resulted in savings when the BGC price was less than $3,000. The simplified strategy (ii) reduced absolute rate of invasive procedures by 10% and improved quality‐adjusted life expectancy, producing an incremental cost‐effectiveness ratio of $10,109 per QALY. In patients with indeterminate nodules, both BGC strategies reduced unnecessary invasive procedures at high risk of adverse events. Moreover, compared to the standard practice, the simplified use of BGC for central and peripheral lesions resulted in larger QALYs gains at acceptable cost. The location‐based is cost‐saving if the price of classifier declines.
Optimal Sizing of Hybrid Microgrid in a Remote Island Considering Advanced Direct Load Control for Demand Response and Low Carbon Emission

Optimal sizing of the power system can drastically reduce the total cost, which is challenging due to the fluctuation in output power of RE (primarily wind and solar) and pollution from thermal generators. The main purpose of this study is to cope with this output power uncertainty of renewables by considering ADLC, residential PV, and BESS at the lowest cost and with the least amount of carbon emission, while putting less burden on consumers by minimizing the IL. This paper optimizes the cost and carbon emission function of a hybrid energy system comprising PV, WG, BESS, and DG at Aguni Island, Japan, using a multi-objective optimization model. To solve the proposed problem in the presence of ADLC, the ϵ-constraint method and MILP are utilized. After obtaining all possible solutions, the FSM selects the best possible solution among all solutions. The result shows that while case 1 has a lower energy cost than the other cases, the quantity of IL is quite significant, putting customers in a burden. In case 2 and case 3, the total energy cost is 11.23% and 10% higher than case 1, respectively, but the sum of the IL is 99% and 95.96% lower than case 1 as the ADLC is applied only for the consumers who have residential PV and BESS, which can reflect the importance of residential PV and BESS. The total cost of case 3 is 1.72% lower than case 2, but IL is higher because sometimes home PV power will be used to charge the home BESS.
Analysis of the spectral dependent microwave characteristics of 1.3 μm DFB Laser at different temperatures

We have demonstrated a 1.3 μm DFB laser with a threshold current of 20 mA and a slope efficiency of over 0.25 W/A for high-power and free-space communication. Even under high-temperature conditions, it can still maintain outstanding single-mode characteristics. We also systematically compare the degree of the wavelength shift at different temperatures and injected currents. At the same time, we observed that the microwave responses are different with the lasing condition is switching between the DFB and Fabry-Perot (FP) mode.
Synthetic Biodegradable Aliphatic Polyester Nanocomposites Reinforced with Nanohydroxyapatite and/or Graphene Oxide for Bone Tissue Engineering Applications

This paper provides review updates on the current development of bionanocomposites with polymeric matrices consisting of synthetic biodegradable aliphatic polyesters reinforced with nanohydroxyaptite (nHA) and/or graphene oxide (GO) nanofillers for bone tissue engineering applications. Biodegradable aliphatic polyesters include poly(lactic acid) (PLA), polycaprolactone (PCL) and copolymers of PLA-PGA (PLGA). Those bionanocomposites have been explored for making 3D porous scaffolds for the repair of bone defects since nHA and GO enhance their bioactivity and biocompatibility by promoting biomineralization, bone cell adhesion, proliferation and differentiation, thus facilitating new bone tissue formation upon implantation. The incorporation of nHA or GO into aliphatic polyester scaffolds also improves their mechanical strength greatly, especially hybrid GO/nHA nanofilllers. Those mechanically strong nanocomposite scaffolds can support and promote cell attachment for tissue growth. Porous scaffolds fabricated from conventional porogen leaching, and thermally induced phase separation have many drawbacks inducing the use of organic solvents, poor control of pore shape and pore interconnectivity, while electrospinning mats exhibit small pores that limit cell infiltration and tissue ingrowth. Recent advancement of 3D additive manufacturing allows the production of aliphatic polyester nanocomposite scaffolds with precisely controlled pore geometries and large pores for the cell attachment, growth, and differentiation in vitro, and the new bone formation in vivo.
Remaining Useful Life Estimation for Turbofan Engine with Transformer-based Deep Architecture

With the development of information technology and sensors, the large industrial system has become a data-rich environment, which leads to the rapid development and application of deep learning for the remaining useful life prediction, especially for the turbofan engine. Currently, the deep architecture of CNN, LSTM have been used to address the RUL estimation of a turbofan engine. However, they are mainly focused on simulation degradation data. The new realistic run-to-failure turbofan engine degradation dataset has been published in 2021, which presents a significant difference from the simulation one. The main challenge is that the flight duration of each cycle is different, which will result in the current deep method hardly used for predicting the RUL for the practical degradation data. To tackle this challenge, we propose a novel Transformer-based model using guiding features to deal with the unfixed-length data. Besides, our G-Transformer model makes use of multi-head attention to access the global features from various representation subspaces. We conduct experiments on turbofan engine degradation data with variable-length input under practical flight conditions. Empirical results and feature visualization via t-SNE indicate the effectiveness of the G-Transformer model for RUL estimation of turbofan engines.
Efficient and Accurate Synapse Detection With Selective Structured Illumination Microscopy on the Putative Regions of Interest of Ultrathin Serial Sections

Critical determinants of synaptic functions include subcellular locations, input sources, and specific molecular characteristics. However, there is not yet a reliable and efficient method that can detect synapses. Electron microscopy is a gold-standard method to detect synapses due to its exceedingly high spatial resolution. However, it requires laborious and time-consuming sample preparation and lengthy imaging time with limited labeling methods. Recent advances in various fluorescence microscopy methods have highlighted fluorescence microscopy as a substitute for electron microscopy in reliable synapse detection in a large volume of neural circuits. In particular, array tomography has been verified as a useful tool for neural circuit reconstruction. To further improve array tomography, we developed a novel imaging method, called “structured illumination microscopy on the putative region of interest on ultrathin sections”, which enables efficient and accurate detection of synapses-of-interest. Briefly, based on low-magnification conventional fluorescence microscopy images, synapse candidacy was determined. Subsequently, the coordinates of the regions with candidate synapses were imaged using super-resolution structured illumination microscopy. Using this system, synapses from the high-order thalamic nucleus, the posterior medial nucleus in the barrel cortex were rapidly and accurately imaged.
Endovascular Interventions in Vascular Complications After Simultaneous Pancreas and Kidney Transplantations: A Single-Center Experience

Background Vascular failures are serious complications in pancreas transplantation. Open surgery is a reliable and quick intervention method, but it carries a risk of infection and bleeding. Endovascular procedures are rare among patients after a SPK, but are becoming more frequently used. One of the main risks of the endovascular approach is that the renal function impairment caused by contrast agent. Material/Methods We performed a retrospective analysis of 200 transplanted pancreases at our center over the last 14 years. The analyses included those patients after pancreas transplantation who required the most challenging vascular interventions and ones that were non-standard for the procedure. Results Severe vascular conditions requiring endovascular intervention were observed in 3% of SPKs. In one retransplanted patient, there was an acute ischemia of the lower extremity due to the narrowing of the common iliac artery following a previous transplantectomy, above the new pancreas graft anastomoses. In another patient, local inflammation led to the disruption of the external iliac artery on the level of transplantectomy, caused severe bleeding, and we had to implement a stent-graft to reconstruct the iliac artery wall. A third patient had a pseudoaneurysm demanding further treatment with a stent-graft implemented into the femoral artery due to a pseudoaneurysm of the right external iliac artery. Conclusions Intravenous interventions in patients with a transplanted or retransplanted pancreas are safe and feasible. It is a technically demanding procedure, but the risk of kidney graft function deterioration, as well as of bleeding due to the high dose of heparin used, is lower than with open vascular surgery.
Dealing with a Missing Sensor in a Multilabel and Multimodal Automatic Affective States Recognition System

Data from multiple sensors can boost the automatic recognition of multiple affective states in a multilabel and multimodal recognition system. At any time, the streaming from any of the contributing sensors can be missing. This work proposes a method for dealing with a missing sensor in a multilabel and multimodal automatic affective states recognition system. The proposed method, called Hot Deck using Conditional Probability Tables (HD-CPT), is incorporated into a multimodal affective state recognition system for compensating the loss of a sensor using the recorded historical information of the sensor and its interaction with the other available sensors. In this work, we consider a multilabel classifier, named Circular Classifier Chain, for the automatic recognition of four states: tiredness, anxiety, pain, and engagement; combined with a multimodal classifier based on three sensors: fingers pressure, hand movements, and facial expressions; which was adapted for coping with the problem of a missing sensor in a virtual rehabilitation platform for post-stroke patients. A dataset of five post-stroke patients who attended ten longitudinal rehabilitation sessions was used for the evaluation. The inclusion of HD-CPT compensated for the loss of one sensor with results above those obtained with only the remaining sensors available. HD-CPT prevents the system from collapsing when a sensor fails, providing continuity of operation with results that attenuate the loss of the sensor. The proposed method HD-CPT can provide robustness for the naturalistic everyday use of an affective states recognition system.