Miracle-dz/UniFAR-FTUs huggingface dataset:
Airborne Dissemination of Bacteria (Enterococci, Staphylococci and Enterobacteriaceae) in a Modern Broiler Farm and Its Environment

Simple Summary In this study, the density and diversity of relevant groups of bacteria at a broiler farm have been studied, in the inside and outside air and in litter samples. A high number of bacteria was detected in the litter and in the inside air, but a low emission of bacteria was found in the outside air. Moreover, the bacteria detected in the outside air decreased with the distance to the farm. A total of 544 isolates were identified from all the samples (146 from the litter, 142 from inside air and 256 from outside air). From these, 162 staphylococci, 176 Enterobacteriaceae, and 190 enterococci were detected. E. hirae was the predominant species and the detection of identical DNA profiles in E. hirae isolates from inside and outside samples suggests the role of the air in bacterial dissemination from the inside of the broiler farm to the immediate environment. It is necessary to consider the relevance of air as a vehicle of disseminating bacteria at the farm level, which can involve potentially pathogenic bacteria and bacteria carrying antimicrobial resistance genes. Abstract The role of the air as a vehicle of bacteria dissemination in the farming environment has been previously reported, but still scarcely studied. This study investigated the bacteria density/diversity of the inside and outside air and of litter samples at a broiler farm. Samples were collected considering two seasons, three outside air distances (50/100/150 m) and the four cardinal directions. Selective media was used for staphylococci, enterococci, and Enterobacteriaceae recovery. A high number of bacteria was detected in the litter (2.9 × 105–5.8 × 107 cfu/g) and in the inside air (>105 cfu/m3), but a low emission of bacteria was evidenced in the outside air (<6 cfu/m3). Moreover, the bacteria detected in the farm’s outside air decreased the further from the farm the sample was taken. A total of 544 isolates were identified by MALDI-TOF (146 from the litter, 142 from inside air and 256 from outside air). From these, 162 staphylococci (14 species; S. saprophyticus 40.7%), 176 Enterobacteriaceae (4 species; E. coli 66%) and 190 enterococci (4 species; E. hirae 83%) were detected. E. hirae was the predominant species, and identical PFGE clones were detected in inside and outside samples. The detection of identical DNA profiles in E. hirae isolates from inside and outside samples suggests the role of the air in bacterial dissemination from the inside of the broiler farm to the immediate environment.
Habitat Characteristics as Potential Drivers of the Angiostrongylus daskalovi Infection in European Badger (Meles meles) Populations

From 2016 to 2020, an investigation was carried out to identify the rate of Angiostrongylus spp. infections in European badgers in Hungary. During the study, the hearts and lungs of 50 animals were dissected in order to collect adult worms, the morphometrical characteristics of which were used for species identification. PCR amplification and an 18S rDNA-sequencing analysis were also carried out. Global and local spatial autocorrelation methods were used to detect high-rated and low-rated infected animal clusters. We conducted a binary logistic regression analysis along with hierarchical agglomerative clustering to determine the relation between selected biotic and abiotic variables, and the prevalence of an A. daskalovi infection. We found a high prevalence (72%) and moderate mean intensity (14.1) of Angiostrongylus sp. infection. Morphology and sequencing revealed that all animals were infected by A. daskalovi. The results of both spatial autocorrelations suggested that the spatial distribution of infected badgers was more spatially clustered than random. The results of an analysis of the correlation between habitat characteristics and infection showed that the infected animals could be associated with dry and open landscape habitats without extended and connected canopy. It is suggested that the territorial behaviour of badgers and the landscape-directed aggregation of potential intermediate hosts might be the drivers of an A. daskalovi infection.
Mapping Global Prevalence of Acinetobacter baumannii and Recent Vaccine Development to Tackle It

Acinetobacter baumannii is a leading cause of nosocomial infections that severely threaten public health. The formidable adaptability and resistance of this opportunistic pathogen have hampered the development of antimicrobial therapies which consequently leads to very limited treatment options. We mapped the global prevalence of multidrug-resistant A. baumannii and showed that carbapenem-resistant A. baumannii is widespread throughout Asia and the Americas. Moreover, when antimicrobial resistance rates of Acinetobacter spp. exceed a threshold level, the proportion of A. baumannii isolates from clinical samples surges. Therefore, vaccines represent a realistic alternative strategy to tackle this pathogen. Research into anti-A. baumannii vaccines have enhanced in the past decade and multiple antigens have been investigated preclinically with varying results. This review summarises the current knowledge of virulence factors relating to A. baumannii–host interactions and its implication in vaccine design, with a view to understanding the current state of A. baumannii vaccine development and the direction of future efforts.
Investigation of Tick-Borne Pathogens in Ixodes ricinus in a Peri-Urban Park in Lombardy (Italy) Reveals the Presence of Emerging Pathogens

Ticks are important vectors of a great range of pathogens of medical and veterinary importance. Lately, the spread of known tick-borne pathogens has been expanding, and novel ones have been identified as (re)emerging health threats. Updating the current knowledge on tick-borne pathogens in areas where humans and animals can be easily exposed to ticks represents a starting point for epidemiological studies and public awareness. A PCR screening for tick-borne pathogens was carried out in Ixodes ricinus ticks collected in a peri-urban recreational park in Ticino Valley, Italy. The presence of Rickettsia spp. , Borrelia burgdorferi senso latu complex, Anaplasma spp. and Babesia spp. was evaluated in a total of 415 I. ricinus specimens. Rickettsia spp. (R monacensis and R. helvetica) were detected in 22.96% of the samples, while B. burgdorferi s.l. complex (B. afzelii and B. lusitaniae) were present in 10.94%. Neoehrlichia mikurensis (1.99%) and Babesia venatorum (0.73%) were reported in the area of study for the first time. This study confirmed the presence of endemic tick-borne pathogens and highlighted the presence of emerging pathogens that should be monitored especially in relation to fragile patients, the difficult diagnosis of tick-borne associated diseases and possible interactions with other tick-borne pathogens.
Effects of tandem injection on compressible turbulent shear layer

Supersonic mixing enhancement using tangential subsonic injection from overlaid slots into supersonic stream is investigated numerically. The numerical analysis was performed with air at freestream Mach number of 2.9 using hydrogen as the injectant at Mach 2. Air is injected at subsonic conditions through an additional slot above the main hydrogen slot. The results are presented for overexpanded, fully expanded, and underexpanded supersonic injectant. Comparisons are made with results obtained using single step injection at similar injectant condtions. Results show that supersonic mixing is remarkably affected by subsonic injection, and the tandem configuration to have superior mixing characteristics over the single step configuration for several hydrogen injection conditions.
Fire Resistance of High-Volume Fly Ash RC Slab Inclusion with Nano-Silica

The study aims to investigate the fire performance of reinforced concrete (RC) slab fabricated from high volume fly ash inclusion with nano-silica (HVFANS) under ISO 834 load curve. The HVFANS concrete slab with dimensions of 1850 mm × 1700 mm × 200 mm was tested via an electrical furnace under an exposing temperature of 1100 °C for 120 min. The slab behaviour was evaluated in terms of residual compressive strength, temperature distribution along its thickness, spalling, and cracks. The results revealed that the slab was capable of maintaining 62.19% of its original compressive strength at room temperature after exposure to the above temperature. Moreover, the distribution of temperature revealed that the temperature of concrete cover and bottom reinforcement was less than 300 °C with a maximum spalling depth of 11 mm within the temperature range of 680 to 840 °C. Furthermore, the thermal conductivity index (K) of the HVFANS concrete was determined, and results indicated that thermal conductivity equalled 0.35 W/mK which is considered low, as compared with other concretes tested in current and previous studies.
Role of Long Non-Coding RNA Polymorphisms in Cancer Chemotherapeutic Response

Genetic polymorphisms are defined as the presence of two or more different alleles in the same locus, with a frequency higher than 1% in the population. Since the discovery of long non-coding RNAs (lncRNAs), which refer to a non-coding RNA with a length of more than 200 nucleotides, their biological roles have been increasingly revealed in recent years. They regulate many cellular processes, from pluripotency to cancer. Interestingly, abnormal expression or dysfunction of lncRNAs is closely related to the occurrence of human diseases, including cancer and degenerative neurological diseases. Particularly, their polymorphisms have been found to be associated with altered drug response and/or drug toxicity in cancer treatment. However, molecular mechanisms are not yet fully elucidated, which are expected to be discovered by detailed studies of RNA–protein, RNA–DNA, and RNA–lipid interactions. In conclusion, lncRNAs polymorphisms may become biomarkers for predicting the response to chemotherapy in cancer patients. Here we review and discuss how gene polymorphisms of lncRNAs affect cancer chemotherapeutic response. This knowledge may pave the way to personalized oncology treatments.
Asymmetric Synthesis of Stereogenic Phosphorus P(V) Centers Using Chiral Nucleophilic Catalysis

Organophosphates have been widely used in agrochemistry, as reagents for organic synthesis, and in biochemistry. Phosphate mimics possessing four unique substituents, and thereby a chirality center, are useful in transition metal catalysis and as nucleotide therapeutics. The catalytic, stereocontrolled synthesis of phosphorus-stereogenic centers is challenging and traditionally depends on a resolution or use of stochiometric auxiliaries. Herein, enantioenriched phosphorus centers have been synthesized using chiral nucleophilic catalysis. Racemic H-phosphinate species were coupled with nucleophilic alcohols under halogenating conditions. Chiral phosphonate products were synthesized in acceptable yields (33–95%) and modest enantioselectivity (up to 62% ee) was observed after identification of an appropriate chiral catalyst and optimization of the solvent, base, and temperature. Nucleophilic catalysis has a tremendous potential to produce enantioenriched phosphate mimics that could be used as prodrugs or chemical biology probes.
Effect of Barley Variety on Feed Intake, Digestibility, Body Weight Gain and Carcass Characteristics in Fattening Lambs

Simple Summary Using a native barley straw as reference, the barley straw from four improved varieties were tested on digestibility and performance in lambs. Differences were observed on feed intake, digestibility, body weight gain and feed-to-gain ratio among lambs fed straws from different barley varieties, pointing to the importance of genetic variation in the feeding value of barley straw. Abstract Twenty lambs (18 ± 0.22 kg initial weight) were blocked by weight and individually assigned into pens to evaluate the effects of barley straw variety on digestibility, growth performance and carcass characteristics. The following four treatments were tested: (1) a local barley straw (as control), (2) HB1963 (high grain and straw yields), (3) Traveller (high straw yielder), and (4) IBON174/03 (high grain yielder). A concentrate (50:50 wheat bran and noug seed cake) was offered constantly (300 DM g), whereas the straw was offered ad libitum. The digestibility trial lasted 22 days (15 days to adapt to dietary treatments and 7 days for sampling). The growth performance trial lasted 90 days. At the end, all of the lambs were slaughtered, and their carcasses were evaluated. The IBON174/03 variety had a higher (p < 0.05) intake of organic matter and crude protein, a higher dry matter and organic matter digestibility than the control, and a faster growth than the control. The feed-to-gain ratio was similar among treatments. The slaughter and empty body weights of lambs in the IBON174/03 group were higher than the control variety (p < 0.05). The present study showed that the feeding value of barley straw can differ substantially between varieties and therefore must be considered in the choice of a barley variety.
Restoring the Patient’s Pre-Arthritic Posterior Slope Is the Correct Target for Maximizing Internal Tibial Rotation When Implanting a PCL Retaining TKA with Calipered Kinematic Alignment

Introduction: The calipered kinematically-aligned (KA) total knee arthroplasty (TKA) strives to restore the patient’s individual pre-arthritic (i.e., native) posterior tibial slope when retaining the posterior cruciate ligament (PCL). Deviations from the patient’s individual pre-arthritic posterior slope tighten and slacken the PCL in flexion that drives tibial rotation, and such a change might compromise passive internal tibial rotation and coupled patellofemoral kinematics. Methods: Twenty-one patients were treated with a calipered KA TKA and a PCL retaining implant with a medial ball-in-socket and a lateral flat articular insert conformity that mimics the native (i.e., healthy) knee. The slope of the tibial resection was set parallel to the medial joint line by adjusting the plane of an angel wing inserted in the tibial guide. Three trial inserts that matched and deviated 2°> and 2°< from the patient’s pre-arthritic slope were 3D printed with goniometric markings. The goniometer measured the orientation of the tibia (i.e., trial insert) relative to the femoral component. Results: There was no difference between the radiographic preoperative and postoperative tibial slope (0.7 ± 3.2°, NS). From extension to 90° flexion, the mean passive internal tibial rotation with the pre-arthritic slope insert of 19° was greater than the 15° for the 2°> slope (p < 0.000), and 15° for the 2°< slope (p < 0.000). Discussion: When performing a calipered KA TKA with PCL retention, the correct target for setting the tibial component is the patient’s individual pre-arthritic slope within a tolerance of ±2°, as this target resulted in a 15–19° range of internal tibial rotation that is comparable to the 15–18° range reported for the native knee from extension to 90° flexion.
Tamoxifen Derivatives Alter Retromer-Dependent Endosomal Tubulation and Sorting to Block Retrograde Trafficking of Shiga Toxins

Shiga toxin 1 and 2 (STx1 and STx2) undergo retrograde trafficking to reach the cytosol of cells where they target ribosomes. As retrograde trafficking is essential for disease, inhibiting STx1/STx2 trafficking is therapeutically promising. Recently, we discovered that the chemotherapeutic drug tamoxifen potently inhibits the trafficking of STx1/STx2 at the critical early endosome-to-Golgi step. We further reported that the activity of tamoxifen against STx1/STx2 is independent of its selective estrogen receptor modulator (SERM) property and instead depends on its weakly basic chemical nature, which allows tamoxifen to increase endolysosomal pH and alter the recruitment of retromer to endosomes. The goal of the current work was to obtain a better understanding of the mechanism of action of tamoxifen against the more disease-relevant toxin STx2, and to differentiate between the roles of changes in endolysosomal pH and retromer function. Structure activity relationship (SAR) analyses revealed that a weakly basic amine group was essential for anti-STx2 activity. However, ability to deacidify endolysosomes was not obligatorily necessary because a tamoxifen derivative that did not increase endolysosomal pH exerted reduced, but measurable, activity. Additional assays demonstrated that protective derivatives inhibited the formation of retromer-dependent, Golgi-directed, endosomal tubules, which mediate endosome-to-Golgi transport, and the sorting of STx2 into these tubules. These results identify retromer-mediated endosomal tubulation and sorting to be fundamental processes impacted by tamoxifen; provide an explanation for the inhibitory effect of tamoxifen on STx2; and have important implications for the therapeutic use of tamoxifen, including its development for treating Shiga toxicosis.
Impact of Influenza A Virus Shutoff Proteins on Host Immune Responses

Influenza A virus (IAV) is a significant human pathogen that causes seasonal epidemics. Although various types of vaccines are available, IAVs still circulate among human populations, possibly due to their ability to circumvent host immune responses. IAV expresses two host shutoff proteins, PA-X and NS1, which antagonize the host innate immune response. By transcriptomic analysis, we previously showed that PA-X is a major contributor for general shutoff, while shutoff active NS1 specifically inhibits the expression of host cytokines, MHC molecules, and genes involved in innate immunity in cultured human cells. So far, the impact of these shutoff proteins in the acquired immune response in vivo has not been determined in detail. In this study, we analyzed the effects of PA-X and NS1 shutoff activities on immune response using recombinant influenza A/California/04/2009 viruses containing mutations affecting the expression of shutoff active PA-X and NS1 in a mouse model. Our data indicate that the virus without shutoff activities induced the strongest T and B cell responses. Both PA-X and NS1 reduced host immune responses, but shutoff active NS1 most effectively suppressed lymphocyte migration to the lungs, antibody production, and the generation of IAV specific CD4+ and CD8+ T cells. NS1 also prevented the generation of protective immunity against a heterologous virus challenge. These data indicate that shutoff active NS1 plays a major role in suppressing host immune responses against IAV infection.
Soil Microbial Indicators within Rotations and Tillage Systems

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses.
Thoracic Aortic Calcification and Pre-Clinical Hypertension by New 2017 ACC/AHA Hypertension Guidelines

The recently revised 2017 American College of Cardiology/American Heart Association (ACC/AHA) hypertension (HTN) guidelines employ a lower blood pressure threshold to define HTN, aiming for earlier prevention of HTN-related cardiovascular diseases (CVD). Thoracic aortic calcification (TAC), a new surrogate marker of aging and aortic medial layer degeneration, and different stages of HTN, according to the 2017 ACC/AHA HTN guidelines, remain unknown. We classified 3022 consecutive asymptomatic individuals enrolled into four HTN categories using the revised 2017 ACC/AHA guidelines: normal blood pressure (NBP), elevated blood pressure (EBP), and stage 1 (S1) and stage 2 (S2) HTN. The coronary artery calcification score and TAC metrics (total Agaston TAC score, total plaque volume (mm3), and mean density (Hounsfield units, HU)) were measured using multi-detector computed tomography. Compared to NBP, a graded and significant increase in the TAC metrics was observed starting from EBP and S1 and S2 HTN, using the new 2017 ACC/AHA guidelines (NBP as reference; all trends: p < 0.001). These differences remained consistent after being fully adjusted. Older age (>50 years), S1 and S2 HTN, prevalent diabetes, and chronic kidney disease (<60 mL/min/1.73 m2) are all independently contributing factors to higher TAC risk using multivariate stepwise logistic regressions (all p ≤ 0.001). The optimal cutoff values of systolic blood pressure, diastolic blood pressure, and pulse pressure were 121, 74, and 45 mmHg, respectively, for the presence of TAC after excluding subjects with known CVD and ongoing HTN medication treatment. Our data showed that the presence of TAC starts at a stage of elevated blood pressure not categorized as HTN from the updated 2017 ACC/AHA hypertension guidelines.