Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology

In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.
Inflammatory infiltration and tissue remodeling in nasal polyps and adjacent mucosa of unaffected sinus.

BACKGROUND This study was designed to explore the characteristics of inflammatory infiltration and tissue remodeling in the adjacent unaffected sinus mucosa of the polyp tissue (ANP). METHODS Nasal polyps (NP) and ANP were obtained from 24 CRSwNP patients who received endoscopic sinus surgery. The frequency and distribution of Eosinophils, T lymphocytes (CD4+ T cells and CD8+ T cells), B lymphocytes, native macrophages, regulatory T cells and the total of inflammatory cells were detected by immunohistochemistry and hematoxylin-eosin stain. The thickness of the basal membrane was evaluated. RESULTS Multivariate analysis of Variance (MANOVA) and F-tests were conducted for each independent variable between two groups. With test criterion alpha = 0.05, significant differences were observed between NP and ANP groups in terms of CD3 (F-Value = 10.47, P-value = 0.0120), CD4 (F-Value = 9.03, P-value = 0.0169), CD8 (F-Value = 17.03, P-value = 0.0033) and regulatory T cells (F-Value = 60.42, P-value <0.0001). Wilks' Lambda test (F-Value = 25.74, P-value = 0.1513) was conducted and no significant difference was observed between the NP group and the ANP group. The percentage of regulatory T cells in ANP was significantly higher than that in NP (3.7110±0.2395 vs 14.6300±1.8360). CONCLUSION ANP and NP may be one disease entity. Treg cells have impacts on the morphology of the tissues and might be a key factor in the further development of ANP.
A Real-Time PCR Screening Assay for Rapid Detection of Listeria Monocytogenes Outbreak Strains

From January 2015 to March 2016, an outbreak of 23 human cases of listeriosis in the Marche region and one human case in the Umbria region of Italy was caused by Listeria monocytogenes strains showing a new pulsotype never described before in Italy. A total of 37 clinical strains isolated from patients exhibiting listeriosis symptoms and 1374 strains correlated to the outbreak were received by the Italian National Reference Laboratory for L. monocytogenes (It NRL Lm) of Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise (IZSAM) for outbreak investigation. A real-time PCR assay was purposely designed for a rapid screening of the strains related to the outbreak. PCR-positive strains were successively typed through molecular serogrouping, pulsed field gel electrophoresis (PFGE), and Next Generation Sequencing (NGS). Applying the described strategy, based on real-time PCR screening, we were able to considerably reduce time and costs during the outbreak investigation activities.
Magnetic Immobilization of Pichia pastoris Cells for the Production of Recombinant Human Serum Albumin

Magnetic immobilization as a novel technique was used to immobilize recombinant Pichia pastoris (GS115 Albumin) cells to produce human serum albumin (HSA). In this regard, magnetic nanoparticles (MNPs) coated with amino propyl triethoxy silane (APTES) were synthesized. P. pastoris cells were decorated with MNPs via nonspecific interactions. Decorated cells were magneto-responsible and easily harvested by applying an external magnetic field. The efficiency of magnetic immobilization (Ei) for cell removal was in direct relation with the MNP concentration and time of exposure to the magnetic field. By increasing the nanoparticles concentration, cells were harvested in a shorter period. Complete cell removal (Ei ≈ 100) was achieved in ≥0.5 mg/mL of MNPs in just 30 s. HSA is produced in an extremely high cell density (OD ~20) and it is the first time that magnetic immobilization was successfully employed for harvesting such a thick cell suspension. After 5 days of induction the cells, which were immobilized with 0.25 to 1 mg/mL of nanoparticles, showed an increased potency for recombinant HSA production. The largest increase in HSA production (38.1%) was achieved in the cells that were immobilized with 0.5 mg/mL of nanoparticles. These results can be considered as a novel approach for further developments in the P. pastoris-based system.
PIP2 Mediated Inhibition of TREK Potassium Currents by Bradykinin in Mouse Sympathetic Neurons

Bradykinin (BK), a hormone inducing pain and inflammation, is known to inhibit potassium M-currents (IM) and to increase the excitability of the superior cervical ganglion (SCG) neurons by activating the Ca2+-calmodulin pathway. M-current is also reduced by muscarinic agonists through the depletion of membrane phosphatidylinositol 4,5-biphosphate (PIP2). Similarly, the activation of muscarinic receptors inhibits the current through two-pore domain potassium channels (K2P) of the “Tandem of pore-domains in a Weakly Inward rectifying K+ channel (TWIK)-related channels” (TREK) subfamily by reducing PIP2 in mouse SCG neurons (mSCG). The aim of this work was to test and characterize the modulation of TREK channels by bradykinin. We used the perforated-patch technique to investigate riluzole (RIL) activated currents in voltage- and current-clamp experiments. RIL is a drug used in the palliative treatment of amyotrophic lateral sclerosis and, in addition to blocking voltage-dependent sodium channels, it also selectively activates the K2P channels of the TREK subfamily. A cell-attached patch-clamp was also used to investigate TREK-2 single channel currents. We report here that BK reduces spike frequency adaptation (SFA), inhibits the riluzole-activated current (IRIL), which flows mainly through TREK-2 channels, by about 45%, and reduces the open probability of identified single TREK-2 channels in cultured mSCG cells. The effect of BK on IRIL was precluded by the bradykinin receptor (B2R) antagonist HOE-140 (d-Arg-[Hyp3, Thi5, d-Tic7, Oic8]BK) but also by diC8PIP2 which prevents PIP2 depletion when phospholipase C (PLC) is activated. On the contrary, antagonizing inositol triphosphate receptors (IP3R) using 2-aminoethoxydiphenylborane (2-APB) or inhibiting protein kinase C (PKC) with bisindolylmaleimide did not affect the inhibition of IRIL by BK. In conclusion, bradykinin inhibits TREK-2 channels through the activation of B2Rs resulting in PIP2 depletion, much like we have demonstrated for muscarinic agonists. This mechanism implies that TREK channels must be relevant for the capture of information about pain and visceral inflammation.
Time required for haemostasis under pressure from dental extraction socket

Introduction: It is generally expected that the time required for a clot to form in an extraction socket must be similar to that of the average physiological bleeding time (2-9 minutes). However, in dental practice does hemostasis require the full clot to form or does it occur earlier? Conventionally there is no accepted average time range for socket hemostasis with estimates ranging from 20 minutes to 40 minutes. This study is an attempt to quantify the average time period required for hemostasis to occur in an extraction socket. Methodology: 1205 consecutive patients attending the dental clinic and requiring dental extractions were evaluated for the average duration of hemostasis after extraction. Exclusion criteria were children (<15 years), pregnant mothers and patients who had a systemic bleeding disorder or were on anticoagulants. The socket was inspected first after five minutes after an extraction and later at 10 minutes and 15 minutes if bleeding continued. Results: Bleeding from an extraction socket settled in less than five minutes in about 83% of individuals and in 10 minutes in 96.5% of cases. Hence it is expected that in an otherwise normal healthy individual socket compression by biting over gauze for around 10 minutes will produce adequate haemostasis. Prolonged bleeding beyond 10 minutes was rare and was controlled with suturing and pressure applied with a gauze pack in healthy individuals. Conclusion: Checking for hemostasis after placing a pressure pack for 5-10 minutes over an extraction socket is a useful act of risk management before discharge of the patient from the clinic to rule out any hemorrhagic tendency.
Mobility impact and methods of diaphragm monitoring in patients with chronic obstructive pulmonary disease: a systematic review

The objectives of the study were to identify the factors that limit diaphragmatic mobility and evaluate the therapeutic results of the monitoring methods previously used in patients with chronic obstructive pulmonary disease. The PubMed, Web of Science, Scopus, and LILACS databases were used. A gray literature search was conducted with Google scholar. PRISMA was used, and the bias risk analysis adapted from the Cochrane Handbook for clinical trials and, for other studies, the Downs and Black checklist were used. Twenty-five articles were included in the qualitative synthesis analysis on physiotherapeutic techniques and diaphragmatic mobility. Eight clinical trials indicated satisfactory domains, and on the Downs and Black scale, 17 cohort studies were evaluated to have an acceptable score. Different conditions must be observed; for example, for postoperative assessments the supine position is suggested to be the most appropriate position to verify diaphragm excursion, although it has been shown to be associated with difficulty of restriction and matching in samples. Therefore, we identified the need for contemporary adjustments and strategies that used imaging instruments, preferably in the dorsal position. Therapeutic evidence on the association between the instrumental method and diaphragmatic mobility can be controversial. The ultrasound measurements indicated some relevance for different analyses, for pulmonary hyperinflation as well as diaphragm thickness and mobilization, in COPD patients. In particular, the study suggests that the ultrasound technique with B-mode for analysis and M-mode for diaphragmatic excursion be used with a 2 - 5 MHz with the patient in the supine position. However, the methods used to monitor diaphragm excursion should be adapted to the conditions of the patients, and additional investigations of their characteristics should be performed. More selective inclusion criteria and better matching in the samples are very important. In addition, more narrow age, sex and weight categories are important, especially in patients with chronic obstructive pulmonary disease.
Energy Conversion Capacity of Barium Zirconate Titanate

In this study, we investigated the effect of zirconium content on lead-free barium zirconate titanate (BZT) (Ba(ZrxTi1−x)O3, with x = 0.00, 0.01, 0.03, 0.05, and 0.08), which was prepared by the sol–gel method. A single-phase perovskite BZT was obtained under calcination and sintering conditions at 1100 °C and 1300 °C. Ferroelectric measurements revealed that the Curie temperature of BaTiO3 was 399 K, and the transition temperature decreased with increasing zirconium content. At the Curie temperature, Ba(Zr0.03Ti0.97)O3 with a dielectric constant of 19,600 showed the best performance in converting supplied mechanical vibration into electrical power. The experiments focused on piezoelectric activity at a low vibrating frequency, and the output power that dissipated from the BZT system at 15 Hz was 2.47 nW (30 MΩ). The prepared lead-free sol–gel BZT is promising for energy-harvesting applications considering that the normal frequencies of ambient vibration sources are less than 100 Hz.
SUCCESSFUL TREATMENT OF A SEVERE VISION-THREATENING PARADOXICAL TUBERCULOUS REACTION WITH INFLIXIMAB: FIRST PEDIATRIC USE.

A 7-year-old girl with tuberculous (TB) meningitis developed optochiasmatic arachnoiditis, a vision-threatening paradoxical reaction, after starting TB treatment including adjunctive steroid therapy. She was treated with infliximab with complete recovery. This is the first report of the use of a tissue necrosis factor α inhibitor for the treatment of a severe paradoxical TB reaction in a child.
Alpha-Thalassemia Carrier due to –α3.7 Deletion: Not So Silent

Background/Objective: Alpha-thalassemia is one of the most prevalent genetic diseases, with the –α3. 7 deletion being the most common mutation. Molecular studies have suggested mechanisms to explain the mild phenotype of “silent carrier” heterozygotes. However, the correlation between the clinical laboratory picture and the –α3. 7 heterozygous state remains unclear, thus we chose to investigate. Methods: We analyzed the medical files of 192 children evaluated for microcytosis at our tertiary center between 2007 and 2017 and diagnosed as heterozygotes for the –α3. 7 deletion. Additional α-thalassemia mutations, iron deficiency anemia, and β-thalassemia were ruled out. Laboratory parameters were compared to age- and sex-matched reference values. Results: The –α3. 7 carriers had significantly lower Hb and mean corpuscular volume (MCV) than the reference population, and significantly higher red blood cell counts across all age groups. The greatest reduction in Hb level appeared among male adolescents, while MCV was consistently 2 SDs lower than normal in most patients older than 2 years. Conclusion: Heterozygosity for the –α3. 7 deletion was associated with clinically significant microcytosis and mild anemia in our pediatric population. In the absence of iron deficiency and β-thalassemia, this finding provides a diagnosis for mild microcytic anemia, making additional investigations of microcytosis unnecessary.
Cell adhesion in cancer: Beyond the migration of single cells

Homeostasis in healthy tissues strongly relies on cell-to-cell adhesion and cell-to-extracellular matrix interactions. For instance, normal epithelial cells maintain tissue structure by adhering to each other and to the extracellular matrix. The proteins that mediate these distinct interactions are collectively called cell adhesion molecules and are divided into four major groups: cadherins, integrins, selectins, and immunoglobulins. They not only physically anchor cells, but also critically integrate signaling between the extracellular microenvironment and cells. These signals include biochemical cues, as adhesion proteins can both act as ligand-activated receptors and activate mechanotransduction triggered by changes in the physical environment. Molecular mechanisms related to cell adhesion signaling have been extensively studied, especially because mutations and changes in expression of these proteins, particularly cadherins and integrins, are frequently associated with diseases ranging from developmental intellectual disability to cancer. In fact, two major hallmarks of cancer, loss of cell-to-cell adhesion and anchorage-independent growth, are both dependent on cell adhesion molecules. Despite many studies elucidating the relationships between malignant transformation and metastasis and cellular adhesion processes, several areas still await exploration. Here, we highlight recently discovered roles of adhesion molecules in collective cancer cell migration and discuss the utility of three-dimensional models in studying cell-cell adhesion. We also describe recent therapeutic approaches targeting adhesion molecules.
Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Background Knowledge on the molecular epidemiology of Escherichia coli causing E. coli bacteremia (ECB) in the Netherlands is mostly based on extended-spectrum beta-lactamase-producing E. coli (ESBL-Ec). We determined differences in clonality and resistance and virulence gene (VG) content between non-ESBL-producing E. coli (non-ESBL-Ec) and ESBL-Ec blood isolates with different epidemiological characteristics. Materials/methods A random selection of non-ESBL-Ec isolates as well as all available ESBL-Ec blood isolates was obtained from two Dutch hospitals between 2014 and 2016. Whole genome sequencing was performed to infer sequence types (STs), serotypes, acquired antibiotic resistance genes and VG scores, based on presence of 49 predefined putative pathogenic VG. Results ST73 was most prevalent among the 212 non-ESBL-Ec (N=26, 12.3%) and ST131 among the 69 ESBL-Ec (N=30, 43.5%). Prevalence of ST131 among non-ESBL-Ec was 10.4% (N=22, P value < 0.001 compared to ESBL-Ec). O25:H4 was the most common serotype in both non-ESBL-Ec and ESBL-Ec. Median acquired resistance gene counts were 1 (IQR 1 – 6) and 7 (IQR 4 – 9) for non-ESBL-Ec and ESBL-Ec, respectively (P value < 0.001). Among non-ESBL-Ec, acquired resistance gene count was highest among blood isolates from a primary gastro-intestinal focus (median 4, IQR 1 – 8). Median VG scores were 13 (IQR 9 – 20) and 12 (IQR 8 – 14) for non-ESBL-Ec and ESBL-Ec, respectively (P value = 0.002). VG scores among non-ESBL-Ec from a primary urinary focus (median 15, IQR 11 – 21) were higher compared to non-ESBL-Ec from a primary gastro-intestinal (median 10, IQR 6 – 13) or hepatic-biliary focus (median 11, IQR 5 – 18) (P values = 0.007 and 0.036, respectively). VG content varied between different E. coli STs. Conclusions Non-ESBL-Ec and ESBL-Ec blood isolates from two Dutch hospitals differed in clonal distribution, resistance gene and VG content. Also, resistance gene and VG content differed between non-ESBL-Ec from different primary foci of ECB.
Integrating Benzenesulfonic Acid Pretreatment and Bio-Based Lignin-Shielding Agent for Robust Enzymatic Conversion of Cellulose in Bamboo

A hydrotrope-based pretreatment, benzenesulfonic acid (BA) pretreatment, was used to fractionate bamboo in this work. With optimized content (80 wt %) of BA in pretreatment liquor, about 90% of lignin and hemicellulose could be removed from bamboo under mild conditions (95 °C, 30 min or 80 °C, 60 min). The potential accessibility of BA pretreated substrate to cellulase was thus significantly improved and was also found to be much higher than those of acidic ethanol and dilute acid pretreatments. But the deposition of lignin on the surface of solid substrates, especially the BA pretreated substrate, was also observed, which showed a negative effect on the enzymatic hydrolysis efficiency. The addition of inexpensive soy protein, a bio-based lignin-shielding agent, could readily overcome this negative effect, leading the increase of enzymatic conversion of cellulose in BA pretreated substrate from 37% to 92% at a low cellulase loading of 4 FPU/g glucan. As compared to acidic ethanol and dilute acid pretreatments, the combination of BA pretreatment and soy protein could not only stably improve the efficiency of non-cellulose components removal, but also could significantly reduce the loading of cellulase.
The Consumption of Two or Three Meals per Day with Adequate Protein Content Is Associated with Lower Risk of Physical Disability in Mexican Adults Aged 60 Years and Older

Adequate protein intake per day has been associated with a lower risk of physical disability; however, if adequate protein intake per meal is also associated is unknown. The purpose of this study was to analyze the association between adequate protein intake per meal and physical disability in daily living activities in Mexican adults aged ≥60 years. We assessed the number of meals per day with an adequate protein content (24 h dietary recall), the presence of physical disability in daily living activities (two validated questionnaires), and their association in 187 participants through logistic regression. Consuming two or three meals per day with ≥30 g each was associated with lower risk of physical disability on Transportation (OR [95% CI]: 0.06 [0.01–0.50], p = 0.01), Shopping (0.05 [0.01–0.40], p = 0.004), Feeding (0.06 [0.01–0.74], p = 0.028), and Transfer (0.09 [0.01–0.98], p = 0.048). On the other hand, consuming two or three meals per day with ≥0.4 g/kg each was associated with lower risk of physical disability on Shopping (0.21 [0.05–0.89], p = 0.034) and Transportation (0.12 [0.03–0.48], p = 0.003). The consumption of two or three meals per day with adequate protein content is associated with lower risk of physical disability in Mexican adults aged 60 years and older.
Gamma Tocopherol Reduced Chemotherapeutic-Induced ROS in an Ovarian Granulosa Cell Line, But Not in Breast Cancer Cell Lines In Vitro

Doxorubicin and cyclophosphamide are used to treat breast cancer, but they also cause infertility through off-target cytotoxicity towards proliferating granulosa cells that surround eggs. Each chemotherapeutic generates reactive oxygen species (ROS) but the effects of the combination, or the antioxidants alpha (αToc) and gamma tocopherol (γToc) on ROS in breast cancer or ovarian cells are unknown. Human breast cancer (MCF7, T47D) and ovarian cancer (OVCAR, COV434) cells were loaded with DCDFA and exposed (1, 2, 3, 24 h) to the MCF7-derived EC25 values of individual agents, or to combinations of these. ROS were quantified and viable cells enumerated using crystal violet or DAPI. Each chemotherapeutic killed ~25% of MCF7, T47D and OVCAR cells, but 57 ± 2% (doxorubicin) and 66 ± 2% (cyclophosphamide) of the COV434 granulosa cells. The combined chemotherapeutics decreased COV434 cell viability to 34 ± 5% of control whereas doxorubicin + cyclophosphamide + γToc reduced ROS within 3 h (p < 0.01) and reduced cytotoxicity to 54 ± 4% (p < 0.05). αToc was not cytotoxic, whereas γToc killed ~25% of the breast cancer but none of the ovarian cells. Adding γToc to the combined chemotherapeutics did not change ROS or cytotoxicity in MCF7, T47D or OVCAR cells. The protection γToc afforded COV434 granulosa cells against chemotherapy-induced ROS and cytotoxicity suggests potential for fertility preservation.