Miracle-dz/UniFAR-FTUs huggingface dataset:
Determination of Antimicrobial Resistance Patterns in Salmonella from Commercial Poultry as Influenced by Microbiological Culture and Antimicrobial Susceptibility Testing Methods

Monitoring antimicrobial resistance of foodborne pathogens in poultry is critical for food safety. We aimed to compare antimicrobial resistance phenotypes in Salmonella isolated from poultry samples as influenced by isolation and antimicrobial susceptibility testing methods. Salmonella isolates were cultured from a convenience sample of commercial broiler ceca with and without selective broth enrichment, and resistance phenotypes were determined for 14 antimicrobials using the Sensititre® platform and a qualitative broth breakpoint assay. The broth breakpoint method reported higher resistance to chloramphenicol, sulfisoxazole, and the combination of trimethoprim and sulfamethoxazole, and lower resistance to streptomycin as compared to the Sensititre® assay in trial one. Selective enrichment of samples containing Salmonella in Rappaport-Vassiliadis broth reported lowered detectable resistance to amoxicillin/clavulanic acid, ampicillin, azithromycin, cefoxitin, ceftriaxone, nalidixic acid, and meropenem, and increased resistance to streptomycin and tetracycline than direct-plating samples in trial one. Using matched isolates in trial two, the Sensititre® assay reported higher resistance to chloramphenicol and gentamicin, and lower resistance to nalidixic acid as compared to the broth breakpoint method. These results suggest methodology is a critical consideration in the detection and surveillance of antimicrobial resistance phenotypes in Salmonella isolates from poultry samples and could affect the accuracy of population or industry surveillance insights and intervention strategies.
Diagnostic Yield of Endoscopic Ultrasound-Guided Liver Biopsy in Comparison to Percutaneous Liver Biopsy: A Two-Center Experience

Simple Summary Traditionally, liver biopsy has been performed by percutaneous radiology-guided methods. Advances in endoscopic ultrasound have demonstrated the efficacy of endoscopic based techniques for liver biopsy. Studies comparing both methods are scarce and have conflicting results. Our study compares percutaneous and endoscopic ultrasound methods for liver biopsy. Our analysis shows no evidence to support the wide use of endoscopic ultrasound. Percutaneous liver biopsy remains the sampling method of choice in this field. Abstract There is scarce and conflicting evidence on the comparison between endoscopic ultrasound (EUS) and percutaneous (PC)-guided liver biopsy (LB). The aim of this study was to compare the two approaches in a series of patients with parenchymal and focal liver lesions. Fifty-four patients undergoing EUS-LB in two high-volume centers between 2017 and 2021 were compared to 62 patients who underwent PC-LB. The primary outcome was diagnostic adequacy rate. The secondary outcomes were diagnostic accuracy, total sample length (TSL), number of complete portal tracts (CPTs), procedural duration, and adverse events. Variables were compared using the Chi-square and Mann–Whitney test. Median age was 56 years (interquartile range 48–69) in the EUS-LB group and 54 years (45–67) in the PC-LB group with most patients being male. Indication for LB was due to parenchymal disease in 50% of patients, whereas the other patients underwent LB due to focal liver lesions. Diagnostic adequacy was 100% in PC-LB and 94.4% in the EUS-LB group (p = 0.74), whereas diagnostic accuracy was 88.8% in the EUS-LB group and 100% in the PC-LB group (p = 0.82). Median TSL was significantly greater in the PC-LB group (27.4 mm, IQR 21–29) when compared to the EUS-LB group (18.5 mm, 10.1–22.4; p = 0.02). The number of complete portal tracts was 21 (11–24) in the PC-LB group and 18.5 (10–23.2) in EUS-LB group (p = 0.09). EUS-LB was a significantly longer procedure (7 min, 5–11 versus 1 min, 1–3 of PC-LB; p < 0.001) and no evidence of adverse events was observed in any of the study groups. These results were confirmed in the subgroup analysis performed according to an indication for LB (parenchymal disease versus focal lesion). Although PC-LB yielded specimens with greater TSL, diagnostic adequacy and accuracy were similar between the two procedures.
Quantitative Assessment of Trout Fish Spoilage with a Single Nanowire Gas Sensor in a Thermal Gradient

The response of a single tin oxide nanowire was collected at different temperatures to create a virtual array of sensors working as a nano-electronic nose. The single nanowire, acting as a chemiresistor, was first tested with pure ammonia and then used to determine the freshness status of trout fish (Oncorhynchus mykiss) in a rapid and non-invasive way. The gas sensor reacts to total volatile basic nitrogen, detecting the freshness status of the fish samples in less than 30 s. The sensor response at different temperatures correlates well with the total viable count (TVC), demonstrating that it is a good (albeit indirect) way of measuring the bacterial population in the sample. The nano-electronic nose is not only able to classify the samples according to their degree of freshness but also to quantitatively estimate the concentration of microorganisms present. The system was tested with samples stored at different temperatures and classified them perfectly (100%), estimating their log(TVC) with an error lower than 5%.
Maternal Folic Acid Intake and Methylation Status of Genes Associated with Ventricular Septal Defects in Children: Case–Control Study

Background: DNA methylation is the best epigenetic mechanism for explaining the interactions between nutrients and genes involved in intrauterine growth and development programming. A possible contributor of methylation abnormalities to congenital heart disease is the folate methylation regulatory pathway; however, the mechanisms and methylation patterns of VSD-associated genes are not fully understood. Objective: To determine if maternal dietary intake of folic acid (FA) is related to the methylation status (MS) of VSD-associated genes (AXIN1, MTHFR, TBX1, and TBX20). Methods: Prospective case–control study; 48 mothers and their children were evaluated. The mothers’ dietary variables were collected through a food frequency questionnaire focusing on FA and the consumption of supplements with FA. The MS of promoters of genes was determined in the children. Results: The intake of FA supplements was significantly higher in the control mothers. In terms of maternal folic acid consumption, significant differences were found in the first trimester of pregnancy. Significant differences were observed in the MS of MTHFR and AXIN1 genes in VSD and control children. A correlation between maternal FA supplementation and MS of AXIN1 and TBX20 genes was found in control and VSD children, respectively. Conclusions: A lower MS of AXIN1 genes and a higher MS of TBX20 genes is associated with FA maternal supplementation.
Fetal Zone Steroids and Estrogen Show Sex Specific Effects on Oligodendrocyte Precursor Cells in Response to Oxidative Damage

Oxygen causes white matter damage in preterm infants and male sex is a major risk factor for poor neurological outcome, which speculates the role of steroid hormones in sex-based differences. Preterm birth is accompanied by a drop in 17β-estradiol (E2) and progesterone along with increased levels of fetal zone steroids (FZS). We performed a sex-based analysis on the FZS concentration differences in urine samples collected from preterm and term infants. We show that, in preterm urine samples, the total concentration of FZS, and in particular the 16α-OH-DHEA concentration, is significantly higher in ill female infants as compared to males. Since we previously identified Nup133 as a novel target protein affected by hyperoxia, here we studied the effect of FZS, allopregnanolone (Allo) and E2 on differentiation and Nup133 signaling using mouse-derived primary oligodendrocyte progenitor cells (OPCs). We show that the steroids could reverse the effect of hyperoxia-mediated downregulation of Nup133 in cultured male OPCs. The addition of FZS and E2 protected cells from oxidative stress. However, E2, in presence of 16α-OH-DHEA, showed a negative effect on male cells. These results assert the importance of sex-based differences and their potential implications in preterm stress response.
Near-Infrared Reflectance Spectroscopy for Predicting the Phospholipid Fraction and the Total Fatty Acid Composition of Freeze-Dried Beef

Research on fatty acids (FA) is important because their intake is related to human health. NIRS can be a useful tool to estimate the FA of beef but due to the high moisture and the high absorbance of water makes it difficult to calibrate the analyses. This work evaluated near-infrared reflectance spectroscopy as a tool to assess the total fatty acid composition and the phospholipid fraction of fatty acids of beef using freeze-dried meat. An average of 22 unrelated pure breed young bulls from 15 European breeds were reared on a common concentrate-based diet. A total of 332 longissimus thoracis steaks were analysed for fatty acid composition and a freeze-dried sample was subjected to near-infrared spectral analysis. 220 samples (67%) were used as a calibration set with the remaining 110 (33%) being used for validation of the models obtained. There was a large variation in the total FA concentration across the animals giving a good data set for the analysis and whilst the coefficient of variation was nearly 68% for the monounsaturated FA it was only 27% for the polyunsaturated fatty acids (PUFA). PLS method was used to develop the prediction models. The models for the phospholipid fraction had a low R2p and high standard error, while models for neutral lipid had the best performance, in general. It was not possible to obtain a good prediction of many individual PUFA concentrations being present at low concentrations and less variable than other FA. The best models were developed for Total FA, saturated FA, 9c18:1 and 16:1 with R2p greater than 0.76. This study indicates that NIRS is a feasible and useful tool for screening purposes and it has the potential to predict most of the FA of freeze-dried beef.
The Influence of Sewage Sludge Content and Sintering Temperature on Selected Properties of Lightweight Expanded Clay Aggregate

Wastewater treatment processes produce sewage sludge (SS), which, in line with environmental sustainability principles, can be a valuable source of matter in the production of lightweight expanded clay aggregate (LECA). The literature on the influence of SS content and sintering temperature on the properties of LECA is scarce. This paper aims to statistically evaluate the effects of SS content and sintering temperature on LECA physical properties. Total porosity, pore volume, and apparent density were determined with the use of a density analyzer. A helium pycnometer was utilized to determine the specific density. Closed porosity was calculated. The test results demonstrated a statistically significant influence of the SS content on the specific density and water absorption of LECA. The sintering temperature had a significant effect on the specific density, apparent density, total porosity, closed porosity, total volume of pores, and water absorption. It was proved that a broad range of the SS content is admissible in the raw material mass for the production of LECA.
Whole Body Cryotherapy and Hyperbaric Oxygen Treatment: New Biological Treatment of Depression? A Systematic Review

Treatment with antidepressants is often insufficiently effective, especially in treatment-resistant depression. In such a situation, it is possible to change the drug, add a second antidepressant, or use pharmacological and non-pharmacological methods of augmenting the effect of pharmacotherapy. New methods that may fall into the scope of multi-module depression treatment as an augmentation of depression treatment are whole body cryotherapy (WBC) and hyperbaric oxygen treatment (HBOT). 545 records were selected and analyzed for these two treatments and finally three clinical trials were selected for analysis. The review also includes data on the possibility of using WBC and HBOT in somatic indications and in organic mental syndromes. Despite the small number of studies on the effectiveness of WBC or HBOT in depression, the current data show that both methods may be effective in the treatment of depression. WBC may be effective in the augmentation of antidepressants, and additionally, it is a method in which a quick antidepressant effect is obtained. HBOT may be effective in endogenous depression, just as it is effective in the treatment of somatic depression symptoms. The results are very preliminary, but if confirmed in subsequent studies, both WBC and HBOT may become new treatment options in treating depression. The authors point to the need and directions for further research into these treatment methods as an augmentation strategy for pharmacological treatment of depression.
Microglia Morphological Changes in the Motor Cortex of hSOD1G93A Transgenic ALS Mice

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of spinal motor neurons as well as corticospinal (CSN) large pyramidal neurons within cortex layer V. An intense microglia immune response has been associated with both upper and lower motor neuron degeneration in ALS patients, whereas microgliosis occurrence in the motor cortex of hSOD1G93A mice—the best characterized model of this disease—is not clear and remains under debate. Since the impact of microglia cells in the neuronal environment seems to be crucial for both the initiation and the progression of the disease, here we analyzed the motor cortex of hSOD1G93A mice at the onset of symptoms by the immunolabeling of Iba1/TMEM119 double positive cells and confocal microscopy. By means of Sholl analysis, we were able to identify and quantify the presence of presumably activated Iba1/TMEM119-positive microglia cells with shorter and thicker processes as compared to the normal surveilling and more ramified microglia present in WT cortices. We strongly believe that being able to analyze microglia activation in the motor cortex of hSOD1G93A mice is of great importance for defining the timing and the extent of microglia involvement in CSN degeneration and for the identification of the initiation stages of this disease.
Detection of Aberrant Glycosylation of Serum Haptoglobin for Gastric Cancer Diagnosis Using a Middle-Up-Down Glycoproteome Platform

Gastric cancer is a frequently occurring cancer and is the leading cause of cancer-related deaths. Recent studies have shown that aberrant glycosylation of serum haptoglobin is closely related to gastric cancer and has enormous potential for use in diagnosis. However, there is no platform with high reliability and high reproducibility to comprehensively analyze haptoglobin glycosylation covering microheterogeneity to macroheterogeneity for clinical applications. In this study, we developed a middle-up-down glycoproteome platform for fast and accurate monitoring of haptoglobin glycosylation. This platform utilizes an online purification of LC for sample desalting, and an in silico haptoglobin glycopeptide library constructed by combining peptides and N-glycans to readily identify glycopeptides. In addition, site-specific glycosylation with glycan heterogeneity can be obtained through only a single MS analysis. Haptoglobin glycosylation in clinical samples consisting of healthy controls (n = 47) and gastric cancer patients (n = 43) was extensively investigated using three groups of tryptic glycopeptides: GP1 (including Asn184), GP2 (including Asn207 and Asn211), and GP3 (including Asn241). A total of 23 individual glycopeptides were determined as potential biomarkers (p < 0.00001). In addition, to improve diagnostic efficacy, we derived representative group biomarkers with high AUC values (0.929 to 0.977) through logistic regression analysis for each GP group. It has been found that glycosylation of haptoglobin is highly associated with gastric cancer, especially the glycosite Asn241. Our assay not only allows to quickly and easily obtain information on glycosylation heterogeneity of a target glycoprotein but also makes it an efficient tool for biomarker discovery and clinical diagnosis.
Mesophase behaviour of 1:1 mixtures of 4-n-alkoxyphenylazo benzoic acids bearing terminal alkoxy groups of different chain lengths

ABSTRACT The thermal and mesophase behaviour of all possible 1:1 mixtures (In/Im) formed from any two homologues of 4-n-alkoxyphenylazo benzoic acids bearing different alkoxy chain lengths (n and m vary between 6 and 16 carbons), were investigated by differential scanning calorimetry (DSC) and phases identified by polarised light microscopy (PLM). Phase transitions were investigated as a function of the average alkoxy chain length (=(n + m)/2) of the mixed acids. A comparison, made between the present series and previously investigated simpler analogues, 4-n-alkoxy benzoic acids, revealed that increasing the length of the mesogenic core increased the stabilities of both the smectic C and nematic phases. GRAPHICAL ABSTRACT
Self-Boundary Dissolution in Meditation: A Phenomenological Investigation

A fundamental aspect of the sense of self is its pre-reflective dimension specifying the self as a bounded and embodied knower and agent. Being a constant and tacit feature structuring consciousness, it eludes robust empirical exploration. Recently, deep meditative states involving global dissolution of the sense of self have been suggested as a promising path for advancing such an investigation. To that end, we conducted a comprehensive phenomenological inquiry into meditative self-boundary alteration. The induced states were systematically characterized by changes in six experiential features including the sense of location, agency, first-person perspective, attention, body sensations, and affective valence, as well as their interaction with meditative technique and overall degree of dissolution. Quantitative analyses of the relationships between these phenomenological categories highlighted a unitary dimension of boundary dissolution. Notably, passive meditative gestures of “letting go”, which reduce attentional engagement and sense of agency, emerged as driving the depth of dissolution. These findings are aligned with an enactive approach to the pre-reflective sense of self, linking its generation to sensorimotor activity and attention-demanding processes. Moreover, they set the stage for future phenomenologically informed analyses of neurophysiological data and highlight the utility of combining phenomenology and intense contemplative training for a scientific characterization of processes giving rise to the basic sense of being a bounded self.
The Synergistic Activity and Optimizing Doses of Tigecycline in Combination with Aminoglycosides against Clinical Carbapenem-Resistant Klebsiella pneumoniae Isolates

Carbapenem-resistant Enterobacteriaceae (CRE), especially carbapenem-resistant Klebsiella pneumoniae (CRKP), are among the largest pathogenic threats to humans. The available antibiotic treatment options for combating CRKP are limited. Colistin-resistant Enterobacteriaceae (CoRE) have also been reported worldwide, including in Thailand. Therefore, this study aimed (1) to determine minimum inhibitory concentrations (MICs) and synergistic activities of antibiotics of CRKP, and (2) to determine the probability target of attainment (PTA) and cumulative fraction of response (CFR) using pharmacokinetic/pharmacodynamic (PK/PD) data. Clinical CRKP isolates were obtained from Phramongkutklao Hospital (June to November 2020). Broth microdilution and checkerboard techniques were used to determine the mono- and synergistic activities of antibiotics. Carbapenemase and mcr-1 genes were also identified by polymerase chain reaction (PCR). The optimal antibiotic regimens were evaluated using Monte Carlo simulations. Forty-nine CRKP isolates were collected, 40 of which were CoRKP strains. The MIC50 and MIC90 of tigecycline, amikacin, and gentamicin were 1 and 2 µg/mL, 4 and 16 µg/mL, and 0.25 and 4 µg/mL, respectively. None of any isolates expressed the mcr-1 gene, whereas blaOXA-48 (53.1%) and blaOXA-48 plus blaNDM (42.9%) were detected. Synergistic activity was observed in 8.2% of isolates for tigecycline combined with amikacin or gentamicin. Additive activity was observed in 75.5% of isolates for tigecycline-amikacin and 69.4% for tigecycline-gentamicin, and no antagonism was observed. High-dose antibiotic regimens achieved the PTA target. The general recommended dose of combination regimens began with 200 mg tigecycline and 25 mg/kg amikacin, or 7 mg/kg gentamicin, followed by 100 mg tigecycline every 12 h and 15 mg/kg amikacin or 5 mg/kg gentamicin every 24 h. In conclusion, tigecycline plus aminoglycosides might be a potential regimen against CRKP and CoRKP. The appropriate combination regimen based on MIC-based dose adjustment can improve optimal antibiotic dosing. Further research via clinical studies will be necessary to confirm these results.
Proteomic Analysis of Synovial Fibroblasts and Articular Chondrocytes Co-Cultures Reveals Valuable VIP-Modulated Inflammatory and Degradative Proteins in Osteoarthritis

Osteoarthritis (OA) is the most common musculoskeletal disorder causing a great disability and a reduction in the quality of life. In OA, articular chondrocytes (AC) and synovial fibroblasts (SF) release innate-derived immune mediators that initiate and perpetuate inflammation, inducing cartilage extracellular matrix (ECM) degradation. Given the lack of therapies for the treatment of OA, in this study, we explore biomarkers that enable the development of new therapeutical approaches. We analyze the set of secreted proteins in AC and SF co-cultures by stable isotope labeling with amino acids (SILAC). We describe, for the first time, 115 proteins detected in SF-AC co-cultures stimulated by fibronectin fragments (Fn-fs). We also study the role of the vasoactive intestinal peptide (VIP) in this secretome, providing new proteins involved in the main events of OA, confirmed by ELISA and multiplex analyses. VIP decreases proteins involved in the inflammatory process (CHI3L1, PTX3), complement activation (C1r, C3), and cartilage ECM degradation (DCN, CTSB and MMP2), key events in the initiation and progression of OA. Our results support the anti-inflammatory and anti-catabolic properties of VIP in rheumatic diseases and provide potential new targets for OA treatment.
Development of Bisphosphonate-Conjugated Antibiotics to Overcome Pharmacodynamic Limitations of Local Therapy: Initial Results with Carbamate Linked Sitafloxacin and Tedizolid

The use of local antibiotics to treat bone infections has been questioned due to a lack of clinical efficacy and emerging information about Staphylococcus aureus colonization of the osteocyte-lacuno canalicular network (OLCN). Here we propose bisphosphonate-conjugated antibiotics (BCA) using a “target and release” approach to deliver antibiotics to bone infection sites. A fluorescent bisphosphonate probe was used to demonstrate bone surface labeling adjacent to bacteria in a S. aureus infected mouse tibiae model. Bisphosphonate and hydroxybisphosphonate conjugates of sitafloxacin and tedizolid (BCA) were synthesized using hydroxyphenyl and aminophenyl carbamate linkers, respectively. The conjugates were adequately stable in serum. Their cytolytic activity versus parent drug on MSSA and MRSA static biofilms grown on hydroxyapatite discs was established by scanning electron microscopy. Sitafloxacin O-phenyl carbamate BCA was effective in eradicating static biofilm: no colony formation units (CFU) were recovered following treatment with 800 mg/L of either the bisphosphonate or α-hydroxybisphosphonate conjugated drug (p < 0.001). In contrast, the less labile tedizolid N-phenyl carbamate linked BCA had limited efficacy against MSSA, and MRSA. CFU were recovered from all tedizolid BCA treatments. These results demonstrate the feasibility of BCA eradication of S. aureus biofilm on OLCN bone surfaces and support in vivo drug development of a sitafloxacin BCA.