Miracle-dz/UniFAR-FTUs huggingface dataset:
Probe Incompatibility in Multiparameter Noisy Quantum Channel Estimation

We derive fundamental bounds on the maximal achievable precision in multiparameter noisy quantum channel estimation, valid under the most general entanglement-assisted adaptive strategy, which are tighter than the bounds obtained by a direct use of single-parameter bounds. This allows us to study the issue of the optimal probe incompatibility in the simultaneous estimation of multiple parameters in generic noisy channels, while so far the issue has been studied mostly in effectively noiseless scenarios (where the Heisenberg scaling is possible). We apply our results to the estimation of both unitary and noise parameters, and indicate models where the fundamental probe incompatibility is present. In particular, we show that in lossy multiple arm interferometry the probe incompatibility is as strong as in the noiseless scenario. Finally, going beyond the multiple-parameter estimation paradigm, we introduce the concept of \emph{random quantum sensing} and show how the tools developed may be applied to multiple channels discrimination problems. As an illustration, we provide a simple proof of the loss of the quadratic advantage of time-continuous Grover algorithm in presence of dephasing or erasure noise.
Probabilistic Rainfall Estimation from Automotive Lidar

Robust sensing and perception in adverse weather conditions remain one of the biggest challenges for realizing reliable autonomous vehicle mobility services. Prior work has established that rainfall rate is a useful measure for the adversity of atmospheric weather conditions. This work presents a probabilistic hierarchical Bayesian model that infers rainfall rate from automotive lidar point cloud sequences with high accuracy and reliability. The model is a hierarchical mixture of experts model, or a probabilistic decision tree, with gating and expert nodes consisting of variational logistic and linear regression models. Experimental data used to train and evaluate the model is collected in a large-scale rainfall experiment facility from both stationary and moving vehicle platforms. The results show prediction accuracy comparable to the measurement resolution of a disdrometer, and the soundness and usefulness of the uncertainty estimation. The model achieves RMSE 2.42mm/h after filtering out uncertain predictions. The error is comparable to the mean rainfall rate change of 3.5mm/h between measurements. Model parameter studies show how predictive performance changes with tree depth, sampling duration, and crop box dimension. A second experiment demonstrates the predictability of higher rainfall above 300mm/h using a different lidar sensor, demonstrating sensor independence.
Active Transport of Hepatotoxic Pyrrolizidine Alkaloids in HepaRG Cells

1,2-unsaturated pyrrolizidine alkaloids (PAs) are secondary plant metabolites occurring as food contaminants that can cause severe liver damage upon metabolic activation in hepatocytes. However, it is yet unknown how these contaminants enter the cells. The role of hepatic transporters is only at the beginning of being recognized as a key determinant of PA toxicity. Therefore, this study concentrated on assessing the general mode of action of PA transport in the human hepatoma cell line HepaRG using seven structurally different PAs. Furthermore, several hepatic uptake and efflux transporters were targeted with pharmacological inhibitors to identify their role in the uptake of the PAs retrorsine and senecionine and in the disposition of their N-oxides (PANO). For this purpose, PA and PANO content was measured in the supernatant using LC-MS/MS. Also, PA-mediated cytotoxicity was analyzed after transport inhibition. It was found that PAs are taken up into HepaRG cells in a predominantly active and structure-dependent manner. This pattern correlates with other experimental endpoints such as cytotoxicity. Pharmacological inhibition of the influx transporters Na+/taurocholate co-transporting polypeptide (SLC10A1) and organic cation transporter 1 (SLC22A1) led to a reduced uptake of retrorsine and senecionine into HepaRG cells, emphasizing the relevance of these transporters for PA toxicokinetics.
Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis

Sphingolipids are essential membrane components and signal molecules, but their regulatory role in cotton embryo growth is largely unclear. In this study, we evaluated the effects of treatment with the sphingolipid synthesis inhibitor fumonisin B1 (FB1), the serine palmityl transferase (SPT) inhibitor myriocin, the SPT sphingolipid product DHS (d18:0 dihydrosphingosine), and the post-hydroxylation DHS product PHS (t18:0 phytosphingosine) on embryo growth in culture, and performed comparative transcriptomic analysis on control and PHS-treated samples. We found that FB1 could inhibit cotton embryo development. At the five-day ovule/embryo developmental stage, PHS was the most abundant sphingolipid. An SPT enzyme inhibitor reduced the fresh weight of embryos, while PHS had the opposite effect. The transcriptomic analysis identified 2769 differentially expressed genes (1983 upregulated and 786 downregulated) in the PHS samples. A large number of transcription factors were highly upregulated, such as zinc finger, MYB, NAC, bHLH, WRKY, MADS, and GRF in PHS-treated samples compared to controls. The lipid metabolism and plant hormone (auxin, brassinosteroid, and zeatin) related genes were also altered. Our findings provide target metabolites and genes for cotton seed improvement.
Revealing the Metabolic Alterations during Biofilm Development of Burkholderia cenocepacia Based on Genome-Scale Metabolic Modeling

Burkholderia cenocepacia is among the important pathogens isolated from cystic fibrosis (CF) patients. It has attracted considerable attention because of its capacity to evade host immune defenses during chronic infection. Advances in systems biology methodologies have led to the emergence of methods that integrate experimental transcriptomics data and genome-scale metabolic models (GEMs). Here, we integrated transcriptomics data of bacterial cells grown on exponential and biofilm conditions into a manually curated GEM of B. cenocepacia. We observed substantial differences in pathway response to different growth conditions and alternative pathway susceptibility to extracellular nutrient availability. For instance, we found that blockage of the reactions was vital through the lipid biosynthesis pathways in the exponential phase and the absence of microenvironmental lysine and tryptophan are essential for survival. During biofilm development, bacteria mostly had conserved lipid metabolism but altered pathway activities associated with several amino acids and pentose phosphate pathways. Furthermore, conversion of serine to pyruvate and 2,5-dioxopentanoate synthesis are also identified as potential targets for metabolic remodeling during biofilm development. Altogether, our integrative systems biology analysis revealed the interactions between the bacteria and its microenvironment and enabled the discovery of antimicrobial targets for biofilm-related diseases.
The Bacterial and Viral Agents of BRDC: Immune Evasion and Vaccine Developments

Bovine respiratory disease complex (BRDC) is a multifactorial disease of cattle which presents as bacterial and viral pneumonia. The causative agents of BRDC work in synergy to suppress the host immune response and increase the colonisation of the lower respiratory tracts by pathogenic bacteria. Environmental stress and/or viral infection predispose cattle to secondary bacterial infections via suppression of key innate and adaptive immune mechanisms. This allows bacteria to descend the respiratory tract unchallenged. BRDC is the costliest disease among feedlot cattle, and whilst vaccines exist for individual pathogens, there is still a lack of evidence for the efficacy of these vaccines and uncertainty surrounding the optimum timing of delivery. This review outlines the immunosuppressive actions of the individual pathogens involved in BRDC and highlights the key issues in the development of vaccinations against them.
Investigation of the Initial Host Response of Naïve Atlantic Salmon (Salmo salar) Inoculated with Paramoeba perurans

Amoebic Gill Disease (AGD), caused by the ectoparasite Paramoeba perurans is characterised by hyperplasia of the gill epithelium and lamellar fusion. In this study, the initial host response of naïve Atlantic salmon (Salmo salar) inoculated with P. perurans was investigated. Using gel-free proteomic techniques and mass spectrometry gill and serum samples were analysed at 7 timepoints (2, 3, 4, 7, 9, 11 and 14 days) post-inoculation with P. perurans. Differential expression of immune related proteins was assessed by comparison of protein expression from each time point against naïve controls. Few host immune molecules associated with innate immunity showed increased expression in response to gill colonisation by amoebae. Furthermore, many proteins with roles in immune signalling, phagocytosis and T-cell proliferation were found to be inhibited upon disease progression. Initially, various immune factors demonstrated the anticipated increase in expression in response to infection in the serum while some immune inhibition became apparent at the later stages of disease progression. Taken together, the pro-immune trend observed in serum, the lack of a robust early immune response in the gill and the diversity of those proteins in the gill whose altered expression negatively impact the immune response, support the concept of a pathogen-derived suppression of the host response.
Perceptions and Attitudes towards Mules in a Group of Soldiers

Simple Summary Working equids play an essential role in the livelihoods of millions of families around the world. The way people, especially their caretakers, perceive them affects attitudes towards them and consequently their welfare. This study aimed to understand the perceptions and attitudes of soldiers towards the mules they work with. For this, psychological constructs, such as empathy and pain perception, and discourse analysis were used. The results show that soldiers’ empathy towards animals is positively associated with their perception of pain and empathy towards humans. Soldiers prefer to work with mules over donkeys and horses, and perceive mules as intelligent and with the best aptitudes for pack work in the mountains, although they perceive them as aggressive. The text analysis shows that soldiers have a good understanding of mules’ nutritional, environmental and health needs but require a better understanding of their behavioral and emotional needs. Finally, they see mules as strong and noble animals, valuable to work under difficult field conditions and an essential component that supports army logistics in the mountain. Future selection and training strategies for soldiers should include behavior and welfare concepts to facilitate the soldier–mule relationship and improve mules’ welfare. Abstract Mules are essential for pack work in mountainous areas, but there is a lack of research on this species. This study intends to assess the perceptions, attitudes, empathy and pain perception of soldiers about mules, to understand the type of human–mule relationship. For this, a survey was applied with closed-ended questions where the empathy and pain perception tools were included and later analyzed through correlations. Open-ended questions were analyzed through text mining. A total of 73 soldiers were surveyed. They had a wide range of ages and years of experience working with equids. Significant positive correlations were found between human empathy, animal empathy and pain perception. Soldiers show a preference for working with mules over donkeys and horses. Text mining analysis shows three clusters associated with the mules’ nutritional, environmental and health needs. In the same line, relevant relations were found for the word “attention” with “load”, “food”, and “harness”. When asked what mules signify for them, two clusters were found, associated with mules’ working capacity and their role in the army. Relevant relations were found between the terms “mountain”, “support”, and “logistics”, and also between “intelligent” and “noble”. To secure mules’ behavioral and emotional needs, future training strategies should include behavior and welfare concepts.
Identifying Conserved Generic Aspergillus spp. Co-Expressed Gene Modules Associated with Germination Using Cross-Platform and Cross-Species Transcriptomics

Aspergillus spp. is an opportunistic human pathogen that may cause a spectrum of pulmonary diseases. In order to establish infection, inhaled conidia must germinate, whereby they break dormancy, start to swell, and initiate a highly polarized growth process. To identify critical biological processes during germination, we performed a cross-platform, cross-species comparative analysis of germinating A. fumigatus and A. niger conidia using transcriptional data from published RNA-Seq and Affymetrix studies. A consensus co-expression network analysis identified four gene modules associated with stages of germination. These modules showed numerous shared biological processes between A. niger and A. fumigatus during conidial germination. Specifically, the turquoise module was enriched with secondary metabolism, the black module was highly enriched with protein synthesis, the darkgreen module was enriched with protein fate, and the blue module was highly enriched with polarized growth. More specifically, enriched functional categories identified in the blue module were vesicle formation, vesicular transport, tubulin dependent transport, actin-dependent transport, exocytosis, and endocytosis. Genes important for these biological processes showed similar expression patterns in A. fumigatus and A. niger, therefore, they could be potential antifungal targets. Through cross-platform, cross-species comparative analysis, we were able to identify biologically meaningful modules shared by A. fumigatus and A. niger, which underscores the potential of this approach.
A Versatile Solid-Phase Approach to the Synthesis of Oligonucleotide Conjugates with Biodegradable Hydrazone Linker

One of the ways to efficiently deliver various drugs, including therapeutic nucleic acids, into the cells is conjugating them with different transport ligands via labile or stable bonds. A convenient solid-phase approach for the synthesis of 5′-conjugates of oligonucleotides with biodegradable pH-sensitive hydrazone covalent bonds is proposed in this article. The approach relies on introducing a hydrazide of the ligand under aqueous/organic media to a fully protected support-bound oligonucleotide containing aldehyde function at the 5′-end. We demonstrated the proof-of-principle of this approach by synthesizing 5′-lipophilic (e.g., cholesterol and α-tocopherol) conjugates of modified siRNA and non-coding RNAs imported into mitochondria (antireplicative RNAs and guide RNAs for Mito-CRISPR/system). The developed method has the potential to be extended for the synthesis of pH-sensitive conjugates of oligonucleotides of different types (ribo-, deoxyribo-, 2′-O-methylribo-, and others) with ligands of different nature.
Survival Rate of Zygomatic Implants for Fixed Oral Maxillary Rehabilitations: A Systematic Review and Meta-Analysis Comparing Outcomes between Zygomatic and Regular Implants

Background: Zygomatic implants have been proposed alone or in combination with premaxillary conventional implants for severe resorbed maxillary atrophy rehabilitation. The aim of the present investigation was to evaluate through a qualitative systematic review and meta-analysis the survival rate of zygomatic implants in conjunction with regular fixtures for maxillary rehabilitation. Methods: The article screening was conducted on the PubMed/Medline and EMBASE electronic databases according to the “Preferred Reporting Items for Systematic Reviews and Meta-Analyses” (PRISMA) guidelines. The scientific papers were included for qualitative analysis and risk-of-bias evaluation. Only the papers that included rehabilitation with zygomatic implants in combination with regular implants were considered for the meta-analysis comparative evaluation of the implant survival rate. Results: The paper search screened a total of 137 papers. After the initial screening, a total of 32 articles were considered for the qualitative analysis. There was a similar implant survival rate between zygomatic and premaxilla regular implants (p = 0.02; Z: 2.26). Conclusions: Zygomatic and conventional implants showed a high long-term survival rate for fixed maxillary rehabilitations, but few included studies reported the marginal bone loss after loading. Further studies are necessary to evaluate the pattern of marginal bone loss between zygomatic and conventional implants after long-term functional loading.
High Dietary Phosphate Exacerbates and Acts Independently of Low Autophagy Activity in Pathological Cardiac Remodeling and Dysfunction

High phosphate contributes to uremic cardiomyopathy. Abnormal autophagy is associated with the development and progression of heart disease. What is unknown is the effects of phosphate on autophagy and whether the ill effects of phosphate on cardiomyocytes are mediated by low autophagy. High (2.0% w/w)-phosphate diet reduced LC3 puncta in cardiomyocytes and ratio of LC3 II/I and increased p62 protein, indicating that autophagy activity was suppressed. Mice with cardiomyocyte-specific deletion of autophagy-related protein 5 (H-atg5−/−) had reduced autophagy only in the heart, developed cardiac dysfunction with hypertrophy and fibrosis, and had a short lifespan. When H-atg5−/− mice were fed a high-phosphate diet, they developed more apoptosis in cardiomyocytes, more severe cardiac remodeling, and shorter lifespan than normal phosphate-fed H-atg5−/− mice, indicating that cardiac phosphotoxicity is imparted independently of atg5. In conclusion, although high phosphate suppresses autophagy, high phosphate and low autophagy independently trigger and additionally amplify cardiac remodeling and dysfunction.
The First Report of a Methicillin-Resistant Staphylococcus aureus Isolate Harboring Type IV SCCmec in Thailand

Methicillin-resistant Staphylococcus aureus (MRSA) is mostly found in Thailand in the hospital as a nosocomial pathogen. This study aimed to report the genetic characterization of a clinical community-acquired MRSA (CA-MRSA) isolate collected from hospitalized patients in Thailand. Among 26 MRSA isolates, S. aureus no. S17 preliminarily displayed the presence of a staphylococcal cassette chromosome mec (SCCmec) type IV pattern. The bacterial genomic DNA was subjected to whole-genome sequencing. Panton–Valentine leukocidin (PVL) production, virulence toxins, and antibiotic resistance genes were identified, and multi-locus sequence typing (MLST) and spa typing were performed. The strain was matched by sequence to MLST type 2885 and spa type t13880. This strain carried type IV SCCmec with no PVL production. Five acquired antimicrobial resistance genes, namely blaZ, mecA, Inu(A), tet(K), and dfrG conferring resistance to β-lactams, lincosamides, tetracycline, and trimethoprim, were identified. The detected toxins were exfoliative toxin A, gamma-hemolysin, leukocidin D, and leukocidin E. Moreover, there were differences in seven regions in CR-MRSA no. S17 compared to CA-MRSA type 300. In summary, we have reported the ST2885-SCCmec IV CA-MRSA clinical strain in Thailand for the first time, highlighting the problem of methicillin resistance in community settings and the consideration in choosing appropriate antibiotic therapy.
A Novel Electrospinning Polyacrylonitrile Separator with Dip-Coating of Zeolite and Phenoxy Resin for Li-ion Batteries

Commercial separators (polyolefin separators) for lithium-ion batteries still have defects such as low thermostability and inferior interface compatibility, which result in serious potential safety distress and poor electrochemical performance. Zeolite/Polyacrylonitrile (Z/PAN) composite separators have been fabricated by electrospinning a polyacrylonitrile (PAN) membrane and then dip-coating it with zeolite (ZSM-5). Different from commercial separators, the Z/PAN composite separators exhibit high electrolyte uptake, excellent ionic conductivity, and prominent thermal stability. Specifically, the Z/PAN-1.5 separator exhibits the best performance, with a high electrolyte uptake of 308.1% and an excellent ionic conductivity of 2.158 mS·cm−1. The Z/PAN-1.5 separator may mechanically shrink less than 10% when held at 180 °C for 30 min, proving good thermal stability. Compared with the pristine PAN separator, the Li/separator/LiFePO4 cells with the Z/PAN-1.5 composite separator have excellent high-rate discharge capacity (102.2 mAh·g−1 at 7 C) and favorable cycling performance (144.9 mAh·g−1 at 0.5 C after 100 cycles). Obviously, the Z/PAN-1.5 separator holds great promise in furthering the safety and performance of lithium-ion batteries.
Are Nanobiosensors an Improved Solution for Diagnosis of Leishmania?

Leishmaniasis is one of the deadliest neglected tropical diseases affecting 12–15 million people worldwide, especially in middle- and low-income countries. Rapid and accurate diagnosis of the disease is important for its adequate management and treatment. Several techniques are available for the diagnosis of leishmaniasis. Among these, parasitological and immunological tests are most widely used. However, in most cases, the utilized diagnostic techniques are not good enough, showing cross-reactivity and reduced accuracy. In recent years, many new methods have been reported with potential for improved diagnosis. This review focuses on the diagnosis of Leishmania exploring the biosensors and nanotechnology-based options for their detection. New developments including the use of nanomaterials as fluorophores, fluorescence quenchers as reducing agents and as dendrimers for signal improvement and amplification, together with the use of aptamers to replace antibodies are described. Future research opportunities to overcome the current limitations on the available diagnostic approaches are also discussed.
D-Fructose Assimilation and Fermentation by Yeasts Belonging to Saccharomycetes: Rediscovery of Universal Phenotypes and Elucidation of Fructophilic Behaviors in Ambrosiozyma platypodis and Cyberlindnera americana

The purpose of this study was to investigate the ability of ascomycetous yeasts to assimilate/ferment d-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the standard set of physiological properties for characterizing yeast species, despite the ubiquitous presence of fructose in the natural environment. In this study, we examined 388 strains of yeast, mainly belonging to the Saccharomycetes (Saccharomycotina, Ascomycota), to determine whether they can assimilate/ferment d-fructose. Conventional methods, using liquid medium containing yeast nitrogen base +0.5% (w/v) of d-fructose solution for assimilation and yeast extract-peptone +2% (w/v) fructose solution with an inverted Durham tube for fermentation, were used. All strains examined (n = 388, 100%) assimilated d-fructose, whereas 302 (77.8%) of them fermented d-fructose. In addition, almost all strains capable of fermenting d-glucose could also ferment d-fructose. These results strongly suggest that the ability to assimilate/ferment d-fructose is a universal phenotype among yeasts in the Saccharomycetes. Furthermore, the fructophilic behavior of Ambrosiozyma platypodis JCM 1843 and Cyberlindnera americana JCM 3592 was characterized by sugar consumption profiles during fermentation.