Miracle-dz/UniFAR-FTUs huggingface dataset:
Coxiella burnetii Shedding in Milk and Molecular Typing of Strains Infecting Dairy Cows in Greece

Ruminants are considered the commonest animal reservoir for human infection of Coxiella burnetii, the Q fever causative agent. Considering the recently described importance of human Q fever in Greece, we aimed at providing the first comprehensive direct evidence of C. burnetii in dairy cows in Greece, including the genetic characterization of strains. The 462 examined dairy farms represented all geographical areas of Greece. One bulk tank milk sample was collected from every farm and tested for the presence of C. burnetii. Molecular genotyping of strains, performed directly on samples, revealed the existence of two separate clades characterized by single nucleotide polymorphism (SNP) genotypes of type 1 and type 2. The two clades were clearly distinguished in multiple locus variable-number tandem repeat analysis (MLVA) by two discriminative loci: MS30 and MS28. Whereas MLVA profiles of SNP-type 2 clade were closely related to strains described in other European cattle populations, the MLVA profile observed within the SNP type 1 clade highlighted a peculiar genetic signature for Greece, related to genotypes found in sheep and goats in Europe. The shedding of C. burnetii bearing this genotype might have yet undefined human epidemiological consequences. Surveillance of the genetic distribution of C. burnetii from different sources is needed to fully understand the epidemiology of Q fever in Greece.
Topical Application of Lidocaine and Bupivacaine to Disbudding Wounds in Dairy Calves: Safety, Toxicology and Wound Healing

Simple Summary Disbudding is a common, but painful procedure performed on calves to prevent horn growth. Tri-Solfen® is a combination local anaesthetic and antiseptic formulation which, applied topically to the disbudding wound, is reported to reduce calf pain. Applied in this manner, the local anaesthetics in Tri-Solfen®, lidocaine and bupivacaine, are reported to be poorly absorbed, resulting in low risk of neurological or cardiotoxic effects. The potential impacts on other blood, urine and tissue parameters and on wound healing when used in this manner, and/or accidental overdose situations are unknown, however. We performed experiments investigating (i) the safety of Tri-Solfen® (including overdose situations) and (ii) the impact of Tri-Solfen® on disbudding wound healing under field conditions. No adverse health effects were observed in Tri-Solfen®-treated animals, even those receiving 5× the recommended dose, with no clinically significant differences in measured parameters between placebo and Tri-Solfen® groups. No negative impacts on wound healing were noted. Conversely, lower levels of bacterial wound colonisation were evident, and there was reduced incidence of abnormal wounds at days 11–12 in Tri-Solfen®-treated animals. Abstract Tri-Solfen® is a combination topical anaesthetic and antiseptic solution containing lidocaine, bupivacaine, adrenaline and cetrimide. Applied to wounds, it is reported to reduce the pain experienced by calves following thermocautery disbudding. While lidocaine and bupivacaine are widely used in medicine, conflicting data exist on the impact of these compounds when applied directly to the surgical wound. To investigate the safety of Tri-Solfen® applied to thermocautery disbudding wounds of calves, experiments were performed to measure (i) the safety of Tri-Solfen® (including in overdose situations); and (ii) the impact of Tri-Solfen® application at recommended doses on disbudding wound healing under field conditions. Haematological, biochemical and urinalysis parameters did not show clinically significant differences between placebo and Tri-Solfen® groups (1×, 3× and 5× dose). No adverse health impacts were reported. Histopathological analysis of wounds noted a reduction in bacterial colonies in Tri-Solfen®-treated wounds. Under field conditions, no negative impacts on wound healing were noted. Conversely, there was reduced incidence of abnormal wounds, with an associated trend toward improved average daily gain at days 11–12 in Tri-Solfen®-treated animals. These data are considered to support the safety of topical anaesthesia, as formulated in Tri-Solfen®, to the thermocautery disbudding wound in calves.
Ultrasound and Bioptic Investigation of Patients with Primary Sjögren’s Syndrome

Primary Sjögren’s syndrome (pSS) is a chronic and heterogeneous disorder characterized by a wide spectrum of glandular and extra-glandular features. The hallmark of pSS is considered to be the immune-mediated involvement of the exocrine glands and B-cell hyperactivation. This leads pSS patients to an increased risk of developing lymphoproliferative diseases, and persistent (>2 months) major salivary gland enlargement is a well-known clinical sign of possible involvement by B cell lymphoma. Better stratification of the patients may improve understanding of the mechanism underlying the risk of lymphoproliferative disorder. Here, we summarize the role of different imaging techniques and a bioptic approach in pSS patients, focusing mainly on the role of salivary gland ultrasonography (SGUS) and a US-guided core needle biopsy (Us-guided CNB) as diagnostic and prognostic tools in pSS patients with persistent parotid swelling.
Functionalized Reduced Graphene Oxide as a Versatile Tool for Cancer Therapy

Cancer is one of the deadliest diseases in human history with extremely poor prognosis. Although many traditional therapeutic modalities—such as surgery, chemotherapy, and radiation therapy—have proved to be successful in inhibiting the growth of tumor cells, their side effects may vastly limited the actual benefits and patient acceptance. In this context, a nanomedicine approach for cancer therapy using functionalized nanomaterial has been gaining ground recently. Considering the ability to carry various anticancer drugs and to act as a photothermal agent, the use of carbon-based nanomaterials for cancer therapy has advanced rapidly. Within those nanomaterials, reduced graphene oxide (rGO), a graphene family 2D carbon nanomaterial, emerged as a good candidate for cancer photothermal therapy due to its excellent photothermal conversion in the near infrared range, large specific surface area for drug loading, as well as functional groups for functionalization with molecules such as photosensitizers, siRNA, ligands, etc. By unique design, multifunctional nanosystems could be designed based on rGO, which are endowed with promising temperature/pH-dependent drug/gene delivery abilities for multimodal cancer therapy. This could be further augmented by additional advantages offered by functionalized rGO, such as high biocompatibility, targeted delivery, and enhanced photothermal effects. Herewith, we first provide an overview of the most effective reducing agents for rGO synthesis via chemical reduction. This was followed by in-depth review of application of functionalized rGO in different cancer treatment modalities such as chemotherapy, photothermal therapy and/or photodynamic therapy, gene therapy, chemotherapy/phototherapy, and photothermal/immunotherapy.
Neutrophil-to-Lymphocyte Ratio Is a Predictive Biomarker in Patients with Epidermal Growth Factor Receptor (EGFR) Mutated Advanced Non-Small Cell Lung Cancer (NSCLC) Treated with Tyrosine Kinase Inhibitor (TKI) Therapy

Simple Summary Though patients with sensitizing epidermal growth factor receptor (EGFR) mutated non-small cell lung cancer have been known to have rapid and durable responses to tyrosine kinase inhibitors, a subset of patients have inferior outcomes and may benefit from therapy escalation. Neutrophil-to-lymphocyte ratio (NLR) has been recognized as one indicator of poor prognosis in patients with various cancers, including non-small cell lung cancer. It is associated with cancer cachexia and treatment resistance. The aim of our study is to assess the serial predictive value of NLR and other markers of cachexia and chronic inflammation in the subset of patients with advanced non-small cell lung cancer who harbor the epidermal growth factor receptor mutation and who are undergoing treatment with tyrosine kinase inhibitor therapy. Abstract Background: First-line treatment for patients with non-small cell lung cancer (NSCLC) with a sensitizing epidermal growth factor receptor (EGFR) mutation is a tyrosine kinase inhibitor (TKI). Despite higher response rates and prolonged progression free survival (PFS) compared with platinum doublet chemotherapy, a subset of these patients do not receive prolonged benefit from these agents. We investigate if the neutrophil-to-lymphocyte ratio (NLR) and other markers of cachexia and chronic inflammation correlate with worse outcomes in these patients. Methods: This study is a retrospective review of 137 patients with advanced EGFR-mutated NSCLC treated with TKIs at Rush University Medical Center and University of Chicago Medicine from August 2011 to July 2019, with outcomes followed through July 2020. The predictive value of NLR and body mass index (BMI) was assessed at the start of therapy, and after 6 and 12 weeks of treatment by univariable and multivariable analyses. Results: On univariable analysis, NLR ≥ 5 or higher NLR on a continuous scale were both associated with significantly worse PFS and overall survival (OS) at treatment initiation, and after 6 or 12 weeks of treatment. On multivariable analysis, NLR ≥ 5 was associated with increased risk of death at 12 weeks of therapy (HR 3.002, 95% CI 1.282–7.029, p = 0.011), as was higher NLR on a continuous scale (HR 1.231, 95% CI 1.063–1.425, p = 0.0054). There was no difference in PFS and OS and amongst BMI categories though number of disease sites and Eastern Cooperative Oncology Group (ECOG) performance status was associated with worse PFS and OS. Conclusions: Patients with NLR ≥ 5 have a worse median PFS and median OS than patients with NLR < 5. NLR may have value as a predictive biomarker and may be useful for selecting patients for therapy intensification in the front-line setting either at diagnosis or after 12 weeks on therapy. NLR needs to be validated prospectively.
Addressing Antiretroviral Drug Resistance with Host-Targeting Drugs—First Steps towards Developing a Host-Targeting HIV-1 Assembly Inhibitor

The concerning increase in HIV-1 resistance argues for prioritizing the development of host-targeting antiviral drugs because such drugs can offer high genetic barriers to the selection of drug-resistant viral variants. Targeting host proteins could also yield drugs that act on viral life cycle events that have proven elusive to inhibition, such as intracellular events of HIV-1 immature capsid assembly. Here, we review small molecule inhibitors identified primarily through HIV-1 self-assembly screens and describe how all act either narrowly post-entry or broadly on early and late events of the HIV-1 life cycle. We propose that a different screening approach could identify compounds that specifically inhibit HIV-1 Gag assembly, as was observed when a potent rabies virus inhibitor was identified using a host-catalyzed rabies assembly screen. As an example of this possibility, we discuss an antiretroviral small molecule recently identified using a screen that recapitulates the host-catalyzed HIV-1 capsid assembly pathway. This chemotype potently blocks HIV-1 replication in T cells by specifically inhibiting immature HIV-1 capsid assembly but fails to select for resistant viral variants over 37 passages, suggesting a host protein target. Development of such small molecules could yield novel host-targeting antiretroviral drugs and provide insight into chronic diseases resulting from dysregulation of host machinery targeted by these drugs.
Production of Enantiopure Chiral Epoxides with E. coli Expressing Styrene Monooxygenase

Styrene monooxygenases are a group of highly selective enzymes able to catalyse the epoxidation of alkenes to corresponding chiral epoxides in excellent enantiopurity. Chiral compounds containing oxirane ring or products of their hydrolysis represent key building blocks and precursors in organic synthesis in the pharmaceutical industry, and many of them are produced on an industrial scale. Two-component recombinant styrene monooxygenase (SMO) from Marinobacterium litorale was expressed as a fused protein (StyAL2StyB) in Escherichia coli BL21(DE3). By high cell density fermentation, 35 gDCW/L of biomass with overexpressed SMO was produced. SMO exhibited excellent stability, broad substrate specificity, and enantioselectivity, as it remained active for months and converted a group of alkenes to corresponding chiral epoxides in high enantiomeric excess (˃95–99% ee). Optically pure (S)-4-chlorostyrene oxide, (S)-allylbenzene oxide, (2R,5R)-1,2:5,6-diepoxyhexane, 2-(3-bromopropyl)oxirane, and (S)-4-(oxiran-2-yl)butan-1-ol were prepared by whole-cell SMO.
Antimicrobial Resistance Genes and Diversity of Clones among ESBL- and Acquired AmpC-Producing Escherichia coli Isolated from Fecal Samples of Healthy and Sick Cats in Portugal

The aim of the study was to analyze the mechanisms of resistance in extended-spectrum beta-lactamase (ESBL)- and acquired AmpC (qAmpC)-producing Escherichia coli isolates from healthy and sick cats in Portugal. A total of 141 rectal swabs recovered from 98 sick and 43 healthy cats were processed for cefotaxime-resistant (CTXR) E. coli recovery (in MacConkey agar supplemented with 2 µg/mL cefotaxime). The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method was used for E. coli identification and antimicrobial susceptibility was performed by a disk diffusion test. The presence of resistance/virulence genes was tested by PCR sequencing. The phylogenetic typing and multilocus sequence typing (MLST) were determined by specific PCR sequencing. CTXR E. coli isolates were detected in seven sick and six healthy cats (7.1% and 13.9%, respectively). Based on the synergy tests, 11 of 13 CTXR E. coli isolates (one/sample) were ESBL-producers (ESBL total rate: 7.8%) carrying the following ESBL genes: blaCTX-M-1 (n = 3), blaCTX-M-15 (n = 3), blaCTX-M-55 (n = 2), blaCTX-M-27 (n = 2) and blaCTX-M-9 (n = 1). Six different sequence types were identified among ESBL-producers (sequence type/associated ESBLs): ST847/CTX-M-9, CTX-M-27, CTX-M-1; ST10/CTX-M-15, CTX-M-27; ST6448/CTX-M-15, CTX-M-55; ST429/CTX-M-15; ST101/CTX-M-1 and ST40/CTX-M-1. Three of the CTXR isolates were CMY-2-producers (qAmpC rate: 2.1%); two of them were ESBL-positive and one ESBL-negative. These isolates were typed as ST429 and ST6448 and were obtained in healthy or sick cats. The phylogenetic groups A/B1/D/clade 1 were detected among ESBL- and qAmpC-producing isolates. Cats are carriers of qAmpC (CMY-2)- and ESBL-producing E. coli isolates (mostly of variants of CTX-M group 1) of diverse clonal lineages, which might represent a public health problem due to the proximity of cats with humans regarding a One Health perspective.
A Very Low CP Level Reduced Diarrhoea and Productivity in Weaner Pigs, but No Differences between Post-Weaning Diets Including Soybean Meal or Soy Protein Concentrate Were Found

Simple Summary Diarrhoea is a challenge after weaning in pigs, and medicinal zinc oxide has been used to decrease this problem. Additionally, soy protein concentrate improves protein digestion and thereby increases growth compared to soybean meal. The aim was to test the effect of different low-protein diets on diarrhoea and productivity. This study demonstrates that a diet with very low-protein levels supplemented with amino acids decreases diarrhoea similar to zinc oxide, but also limits growth performance. Moreover, the study found no effect of low-protein diets with different protein sources. Based on these results, there is potential in feeding extremely low-protein diets to weaned pigs as a tool to decrease diarrhoea and thereby antibiotics usage. Additionally, this study presents an opportunity to use both soy protein concentrate and soybean meal as the main protein source, without affecting pig health and productivity. Abstract Soy protein concentrate improves nutrient utilization and growth performance compared to soybean meal, and diets with a low crude protein (CP) level decreases diarrhoea. The objectives were to (1) test a low CP diet based on different soy products, and (2) to test a very-low CP diet (15.1%) with amino acids (AA) on diarrhoea and productivity. A total of 5,635 weaned pigs (~28 days), were assigned to five dietary treatments; PC (positive control): Standard CP levels (192, 189, 191 g/kg CP) with 2500 ppm ZnO; NC (negative control): Same as PC without ZnO; SP (Soy protein concentrate): Low CP levels (176, 174, 191 g/kg CP); SB (Soybean meal): Low CP levels (177, 176, 191 g/kg CP); and XLA (X-low CP + AA): Very low CP levels (154, 151, 191 g/kg CP) with AA. The PC and XLA diets reduced diarrhoea by 41 and 61%, respectively, compared to the NC group, while no difference between SB and SP were observed. The XLA diet reduced feed intake and daily gain compared with PC and NC, where SP, SB, and XLA had a poorer feed conversion compared with PC. Conclusively, the SP and SB low-protein diets did not reduce diarrhoea or growth performance, whereas the XLA diet decreased both diarrhoea and performance.
A Novel High Throughput, Parallel Infection Assay for Determining the Replication Capacities of 346 Primary HIV-1 Isolates of the Zurich Primary HIV-1 Infection Study in Primary Cells

HIV-1 replication capacity is an important characteristic to understand the replication competence of single variants or virus populations. It can further aid in the understanding of HIV-1 pathogenicity, disease progression, and drug resistance mutations. To effectively study RC, many assays have been established. However, there is still demand for a high throughput replication capacity assay using primary cells which is robust and reproducible. In this study, we established such an assay and validated it using 346 primary HIV-1 isolates from patients enrolled in the Zurich Primary HIV Infection study (ZPHI) and two control viruses, HIV-1 JR-CSFWT and HIV-1 JR-CSFK65R_M184V. Replication capacity was determined by measuring the viral growth on PBMCs over 10 days by longitudinally transferring cell culture supernatant to TZM-bl reporter cells. By utilizing the TZM-bl luciferase reporter assay, we determined replication capacity by measuring viral infectivity. The simplicity of the experimental setup allowed for all 346 primary HIV-1 isolates to be replicated at one time. Although the infectious input dose for each virus was normalized, a broad range of replication capacity values over 4 logs was observed. The approach was confirmed by two repeated experiments and we demonstrated that the reproducibility of the replication capacity values is statistically comparable between the two separate experiments. In summary, these results endorse our high throughput replication capacity assay as reproducible and robust and can be utilized for large scale HIV-1 replication capacity experiments in primary cells.
Effect of Chitosan Inclusion and Dietary Crude Protein Level on Nutrient Intake and Digestibility, Ruminal Fermentation, and N Excretion in Beef Heifers Offered a Grass Silage Based Diet

Simple Summary The level of crude protein offered to beef cattle has an impact on the level of nitrogen excreted into the environment, contributing towards ammonia emissions, which have a negative impact on terrestrial and aquatic ecosystems as well as air pollution. The aim of this study was to investigate the effects of including chitosan with different levels of crude protein on nutrient intake and digestibility, rumen fermentation, and nitrogen excretion in beef heifers offered a grass silage-based diet. Chitosan inclusion reduced nutrient digestibility, whereas feeding the high crude protein diet increased the apparent digestibility of crude protein. Feeding the high crude protein diet increased the amount of nitrogen excreted in the urine, while chitosan inclusion increased the amount of nitrogen excreted in the faeces. The chitosan used in this study had a negative effect on dry matter, organic matter, and crude protein digestibility, while feeding the high crude protein diet increased the amount of nitrogen excreted in the urine, which has a negative effect on the environment. Abstract Nitrogen (N) use efficiency in beef cattle is low (10–20%), resulting in large amounts of N excreted into the environment. The objective of this study was to evaluate the effects of chitosan inclusion and dietary crude protein (CP) level on nutrient intake and digestibility, ruminal fermentation, and N excretion in beef heifers. Eight Belgian Blue × Holstein Friesian cross beef heifers (752 ± 52 kg BW) were used in a 4 × 4 Latin square with a 2 × 2 factorial design. Factors were dietary CP concentration—high CP, 16% (HP) or low CP, 12% (LP)—and chitosan inclusion—0 or 10 g kg−1 dry matter (DM) offered at 50:50 forage concentrate ratio on a dry matter (DM) basis. Apparent total tract digestibility of DM, organic matter (OM), and CP were reduced (p < 0.001) with chitosan inclusion, whereas offering the HP diets increased apparent total tract digestibility of CP (p < 0.001). Offering the HP diets increased urinary N excretion (p < 0.001), while chitosan inclusion increased N excretion in faeces (p < 0.05). Ruminal pH was increased with chitosan inclusion (p < 0.01). There was a CP × chitosan interaction for rumen ammonia (NH3) concentrations (p < 0.05). Including chitosan in the HP diets increased ruminal NH3 concentration while having no effect on the LP diets. Urinary N excretion was increased with increased levels of CP, but chitosan inclusion increased the quantity of N excreted in the faeces.
Synergy Effect of Nano-Organic Palygorskite on the Properties of Star-Shaped SBS-Modified Asphalt

With the rapid development of economic construction, styrene-butadiene-styrene (SBS)-modified asphalt is being more and more widely used in highway engineering, but there are still many deficiencies in the process of its use. In order to further improve its performance for use, nano-organic palygorskite (A-Pal) and star-shaped SBS were compounded to obtain modified asphalt in this study. The high-temperature stability of SBS-modified asphalt was enhanced after incorporation with A-Pal for the high-temperature stability test by a dynamic shear rheometer. The A-Pal should improve the surface free energy and adhesion of SBS-modified asphalt by the water stability test analysis. The aging test shows that A-Pal can reduce the thermal oxygen decomposition of SBS and improve the anti-aging performance and the fatigue resistance of SBS-modified asphalt. A-Pal has a certain improvement effect on the low temperature performance of SBS-modified asphalt as shown by a low temperature crack resistance test. A-Pal-compounded SBS-modified asphalt features good storage stability in normal temperatures with the lowest critical compatibility temperature.