Search Results (15)

Objective: The totally endoscopic approach is on the rise to become the new standard in mitral valve surgery. The aim of this study was to develop a morphometric measurement tool for educational purposes to predict operability with low conversion and high repair rates. Methods: From January 2020 to March 2023, 64 patients underwent totally endoscopic mitral valve repair (TE-MVR). Of these, 15 patients were deemed to be unsuitable for TE-MVR due to narrow space and/or anticipated complex repair techniques and underwent repair through sternotomy (MVR-open). Angio-CT scanning was performed for preoperative planning and measurements of the following: the distance between the sternum and the spine (DSS), the distance between the skin incision and the anterior anulus of the mitral valve (DNM) and the intercostal space at the level of the skin incision (ICS). Results: The repair rate for all patients was 98.7%. In the TE-MVR group, the conversion rate to sternotomy was 3.1%. The 30-day survival was 100%. The DSS was 130.4 ± 18.8 mm and 108.1 ± 17.3 mm, and the DSM 70.7 ± 12.1 mm and 58.5 ± 13.6 mm in the TE-MVR and MVR-open, respectively (p < 0.001). Twenty-one TE-MVR patients were found to be technically demanding due to friction and less freedom to move the instruments. The composite morphometric parameter DSS plus 4xICS minus DNM was 53.3, 39.8 and 25.6 for TE-TMReasy, TE-TMRdemanding and MVR-open, respectively (p < 0.05 and p < 0.01). Conclusions: Surgical skills and a long history of expertise are mandatory to achieve excellent results with a low conversion and high repair rate. The composite morphometric parameter may be an easy tool for educational demands to predict the ease and feasibility of TE-MVR. Full article

Background: Antidepressants are a class of pharmaceuticals utilized for the management of many psychiatric disorders, including depression. A considerable number of antidepressants, particularly selective serotonin reuptake inhibitors (SSRIs), have been documented to demonstrate significant anticancer properties in various cancer cell lines. Objectives: The aim of this study was to evaluate the selective cytotoxic and apoptotic effects of escitalopram oxalate (ES) alone and in combination with etoposide (ET) on ET-resistant A549 (A549/90E) lung cancer cells. Methods: The cytotoxic effects of the drugs were determined by CCK-8, trypan blue, and neutral red assays. Apoptosis was observed by Annexin V fluorescein isothiocyanate (FITC)/PI and mitochondrial membrane potential (ΔΨm) assays. Moreover, the effects of the drugs, alone and in combination, on apoptosis-related proteins, caspase-3, PTEN, and resistance-related P-gP were determined by ELISA. The relationship between drugs and lung cancer was determined with protein–protein interaction (PPI) network analysis. Results: Our results revealed that ES significantly exerted cytotoxic effects on both wild-type and A549/90E cells compared with BEAS-2B cells. The IC₅₀ values of 48.67 and 51.6 μg/mL obtained for ET and ES, respectively, at the end of 24 h of incubation for A549 cells were applied reciprocally for each cell by including BEAS-2B together with the 2xIC₅₀ and ½ IC₅₀ values. The results of each combination were statistically evaluated with combination indices (CIs) obtained using the Compusyn synergistic effect analysis program. Combination doses with a synergistic effect in A549 and A549/90E cells and an antagonistic effect in BEAS-2B cells have been determined as ½ IC₅₀ for ET and ½ IC₅₀ for ES. ET ½ IC₅₀, ES ½ IC₅₀, and an ET ½ IC₅₀ + ES ½ IC₅₀ combination caused 18.37%, 55.19%, and 57.55% death in A549 cells, whereas they caused 44.9%, 22.4%, and 51.94% death in A549/90E cells, respectively. In A549 cells, the combination of ES ½ IC₅₀ and ET ½ IC₅₀ caused increased levels of caspase-3 (p < 0.01) and P-gP (p < 0.001), while PTEN levels remained unchanged. The combination resulted in an increase in caspase-3 (p < 0.001) and PTEN (p < 0.001) amounts, alongside a decrease in P-gP (p < 0.01) levels in A549/90E cells. The death mechanism induced by the combination was found to be apoptotic by Annexin V-FITC and ΔΨm assays. Conclusions: Based on our findings, ES was observed to induce cytotoxic and apoptotic activities in A549/90E cells in vitro. ES in combination therapy is considered to be effective to overcome ET resistance by reducing the amount of P-gP in A549/90E cells. Full article

Timely mitosis is critically important for early embryo development. It is regulated by the activity of the conserved protein kinase CDK1. The dynamics of CDK1 activation must be precisely controlled to assure physiologic and timely entry into mitosis. Recently, a known S-phase regulator CDC6 emerged as a key player in mitotic CDK1 activation cascade in early embryonic divisions, operating together with Xic1 as a CDK1 inhibitor upstream of the Aurora A and PLK1, both CDK1 activators. Herein, we review the molecular mechanisms that underlie the control of mitotic timing, with special emphasis on how CDC6/Xic1 function impacts CDK1 regulatory network in the Xenopus system. We focus on the presence of two independent mechanisms inhibiting the dynamics of CDK1 activation, namely Wee1/Myt1- and CDC6/Xic1-dependent, and how they cooperate with CDK1-activating mechanisms. As a result, we propose a comprehensive model integrating CDC6/Xic1-dependent inhibition into the CDK1-activation cascade. The physiological dynamics of CDK1 activation appear to be controlled by the system of multiple inhibitors and activators, and their integrated modulation ensures concomitantly both the robustness and certain flexibility of the control of this process. Identification of multiple activators and inhibitors of CDK1 upon M-phase entry allows for a better understanding of why cells divide at a specific time and how the pathways involved in the timely regulation of cell division are all integrated to precisely tune the control of mitotic events. Full article

Although data-independent acquisition (DIA) has the ability to identify and quantify all peptides in a sample, highly complex mixed mass spectra present difficulties for accurate peptide and protein identification. Additionally, the correspondence between the precursor and its fragments is broken, making it challenging to perform peptide identification directly using conventional DDA search engines. In this paper, we propose a cosine-similarity-based deconvolution method: CorrDIA. This is achieved by reconstructing the correspondence between precursor and fragment ions based on the consistency of extracted ion chromatograms (XICs). A deisotope peak cluster operation is added and centered on the MS/MS spectrum to improve the accuracy of spectrum interpretation and increase the number of identified peptides. The resulting MS/MS spectra can be identified using any data-dependent acquisition (DDA) sequencing software. The experimental results demonstrate that the number of peptide results increased by 12 percent and 21 percent respectively, and the repetition rate decreased by 12 percent. This reduces mass spectra complexity and difficulties in mass spectra analysis without the need for any mass spectra libraries. Full article

Despite several decades’ effort to detect and identify phytoplasmas (Mollicutes) using PCR and Sanger sequencing focusing on diseased plants, knowledge of phytoplasma biodiversity and vector associations remains highly incomplete. To improve protocols for documenting phytoplasma diversity and ecology, we used DNA extracted from phloem-feeding insects and compared traditional Sanger sequencing with a next-generation sequencing method, Anchored Hybrid Enrichment (AHE) for detecting and characterizing phytoplasmas. Among 22 of 180 leafhopper samples that initially tested positive for phytoplasmas using qPCR, AHE yielded phytoplasma 16Sr sequences for 20 (19 complete and 1 partial sequence) while Sanger sequencing yielded sequences for 16 (11 complete and 5 partial). AHE yielded phytoplasma sequences for an additional 7 samples (3 complete and 4 partial) that did not meet the qPCR threshold for phytoplasma positivity or yielded non-phytoplasma sequences using Sanger sequencing. This suggests that AHE is more efficient for obtaining phytoplasma sequences. Twenty-three samples with sufficient data were classified into eight 16Sr subgroups (16SrI-B, I-F, I-AO, III-U, V-C, IX-J, XI-C, XXXVII-A), three new subgroups (designated as 16SrVI-L, XV-D, XI-G) and three possible new groups. Our results suggest that screening phloem-feeding insects using qPCR and AHE sequencing may be the most efficient method for discovering new phytoplasmas. Full article

Staphylococcus is a major bacterial species that contaminates retail meat products. The objective of this study was to clarify the prevalence, antimicrobial resistance and genetic determinants of Staphylococcus/Mammaliicoccus species in retail ground meat in Japan. From a total of 146 retail ground meat samples (chicken, pork, mixed beef/pork) purchased during a 5-month period, 10 S. aureus and 112 isolates of coagulase-negative staphylococcus (CoNS)/Mammaliicoccus comprising 20 species were recovered. S. aureus isolates were classified into five genetic types, i.e., coa-IIa/ST5, coa-VIc/ST352 (CC97), coa-VIIb/ST398, coa-Xa/ST15, and coa-XIc/ST9, which were all related to those of livestock-associated clones. All the staphylococcal isolates were mecA-negative and mostly susceptible to all the antimicrobials tested, except for ampicillin among S. aureus (resistance proportion; 50%). Among CoNS, the fosfomycin resistance gene fosB was prevalent (30/112; 26.8%), primarily in S. capitis, S. warneri, and S. saprophyticus. Phylogenetic analysis of fosB revealed the presence of seven clusters, showing broad diversity with 65–81% identity among different clusters. In the CoNS isolates from ground meat samples, fosB was assigned into three clusters, and S. saprophyticus harbored the most divergent fosB with three genetic groups. These findings suggested the circulation of multiple fosB-carrying plasmids among some CoNS species. Full article

The analysis of marine lipophilic toxins in shellfish products still represents a challenging task due to the complexity and diversity of the sample matrix. Liquid chromatography coupled with mass spectrometry (LC-MS) is the technique of choice for accurate quantitative measurements in complex samples. By combining unambiguous identification with the high selectivity of tandem MS, it provides the required high sensitivity and specificity. However, LC-MS is prone to matrix effects (ME) that need to be evaluated during the development and validation of methods. Furthermore, the large sample-to-sample variability, even between samples of the same species and geographic origin, needs a procedure to evaluate and control ME continuously. Here, we analyzed the toxins okadaic acid (OA), dinophysistoxins (DTX-1 and DTX-2), pectenotoxin (PTX-2), yessotoxin (YTX) and azaspiracid-1 (AZA-1). Samples were mussels (Mytilus galloprovincialis), both fresh and processed, and a toxin-free mussel reference material. We developed an accurate mass-extracted ion chromatogram (AM-XIC) based quantitation method using an Orbitrap instrument, evaluated the ME for different types and extracts of mussel samples, characterized the main compounds co-eluting with the targeted molecules and quantified toxins in samples by following a standard addition method (SAM). An AM-XIC based quantitation of lipophilic toxins in mussel samples using high resolution and accuracy full scan profiles (LC-HR-MS) is a good alternative to multi reaction monitoring (MRM) for instruments with HR capabilities. ME depend on the starting sample matrix and the sample preparation. ME are particularly strong for OA and related toxins, showing values below 50% for fresh mussel samples. Results for other toxins (AZA-1, YTX and PTX-2) are between 75% and 110%. ME in unknown matrices can be evaluated by comparing their full scan LC-HR-MS profiles with those of known samples with known ME. ME can be corrected by following SAM with AM-XIC quantitation if necessary. Full article

In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification. Full article

Astringency is a complex oral sensation, commonly experienced when dietary polyphenols interact with salivary proteins. Most astringent stimuli alter protein levels, which then require time to be replenished. Although it is standard practice in astringency research to provide breaks in between stimuli, there is limited consensus over the amount of time needed to restore the oral environment to baseline levels. Here we examined salivary protein levels after exposure to 20 mL of a model stimulus (cranberry polyphenol extract, 0.75 g/L CPE) or unsweetened cranberry juice (CJ), over a 10 min period. Whole saliva from healthy subjects (n = 60) was collected at baseline and after 5 and 10 min following either stimulus. Five families of proteins: basic proline-rich proteins (bPRPs); acidic proline-rich proteins (aPRPs); histatins; statherin; and S-type cystatins, were analyzed in whole saliva via HPLC-low resolution-ESI-IT-MS, using the area of the extracted ion current (XIC) peaks. Amylase was quantified via immunoblotting. In comparison to baseline (resting), both stimuli led to a rise in levels of aPRPs (p < 0.000) at 5 min which remained elevated at 10 min after stimulation. Additionally, an interaction of PROP taster status and time was observed, wherein super-tasters had higher levels of amylase in comparison to non-tasters after stimulation with CJ at both timepoints (p = 0.014–0.000). Further, male super-tasters had higher levels of bPRPs at 5 min after stimulation with both CJ and CPE (p = 0.015–0.007) in comparison to baseline. These data provide novel findings of interindividual differences in the salivary proteome that may influence the development of astringency and that help inform the design of sensory experiments of astringency. Full article

Non-targeted mass spectrometry (MS) has become an important method over recent years in the fields of metabolomics and environmental research. While more and more algorithms and workflows become available to process a large number of non-targeted data sets, there still exist few manually evaluated universal test data sets for refining and evaluating these methods. The first step of non-targeted screening, peak detection and refinement of it is arguably the most important step for non-targeted screening. However, the absence of a model data set makes it harder for researchers to evaluate peak detection methods. In this Data Descriptor, we provide a manually checked data set consisting of 255,000 EICs (5000 peaks randomly sampled from across 51 samples) for the evaluation on peak detection and gap-filling algorithms. The data set was created from a previous real-world study, of which a subset was used to extract and manually classify ion chromatograms by three mass spectrometry experts. The data set consists of the converted mass spectrometry files, intermediate processing files and the central file containing a table with all important information for the classified peaks. Full article

Systematic comparison of active ingredients in Sojae semen praeparatum (SSP) during fermentation was performed using ultra-fast liquid chromatography (UFLC)–TripleTOF MS and principal component analysis (PCA). By using this strategy, a total of 25 varied compounds from various biosynthetic groups were assigned and relatively quantified in the positive or negative ion mode, including two oligosaccharides, twelve isoflavones, eight fatty acids, N–(3–Indolylacetyl)–dl–aspartic acid, methylarginine, and sorbitol. Additionally, as the representative constituents, six targeted isoflavones were sought in a targeted manner and accurately quantified using extracted ion chromatograms (XIC) manager (AB SCIEX, Los Angeles, CA, USA) combined with MultiQuant software (AB SCIEX, Los Angeles, CA, USA). During the fermentation process, the relative contents of oligoses decreased gradually, while the fatty acids increased. Furthermore, the accurate contents of isoflavone glycosides decreased, while aglycones increased and reached a maximum in eight days, which indicated that the ingredients converted obviously and regularly throughout the SSP fermentation. In combination with the morphological changes, which meet the requirements of China Pharmacopoeia, this work suggested that eight days is the optimal time for fermentation of SSP from the aspects of morphology and content. Full article

Fluorescent silver nanoclusters (Ag-NCs) are in prominence as novel sensing materials due to their biocompatibility, photostability, and molecule-like optical properties. The present work is carried out on an array (17 sequences) of 16 bases long cytosine rich, single stranded DNA templates 5′-C₃X_iC₃X_iiC₃X_iiiC₃X_iv-3′ where i, ii, iii, iv correspond to T/G/C deoxynucleobases (with default base A). Among all the oligonucleotides, a sequence C₃AC₃AC₃TC₃G (3T4G) has been identified, which grows three different near-infrared-emitting NC species with absorption/emission maxima at ~620/700 (species I), 730/800 (species II), and 830 (Species III) nm, respectively. The nature of the spectral profiles, along with relevant parameters namely absorption maximum ((lambda_{abs}^{max})), emission maximum ((lambda_{em}^{max})), anisotropy (r), lifetime (( au)), circular dichroism spectral data are used to understand the microenvironments of the fluorescent NC species I, II, and III. DNA:Ag stiochiometric, pH and solvent dependent studies proved that i-motif scaffolds with different folding topologies are associated with the growth of these three species and a certain concentration of silver and H⁺ favor the growth of species III. Size exclusion chromatographic measurements provided similar indications that a folded, more compact, classic i-motif template is associated with the formation of the longer NIR (~830 nm) absorbing species. This study provides a more definitive approach to design and obtain a targeted DNA templated Ag-NC with required emission properties for biophysical and cellular applications. Full article

A simple and reliable ultra performance liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry method (UPLC-TOF-MS) was developed and validated for the simultaneous determination of the major bioactive constituents in Acanthopanax senticosus and its extract. The separation of five compounds was performed on a UPLC^TM HSS T3 column (100 mm × 2.1 mm, 1.7 μm) with gradient elution using a mobile phase consisting of 0.1% aqueous formic acid and acetonitrile containing 0.1% formic acid. All targeted compounds (syringin, chlorogenid acid, caffeic acid, eleutheroside E and isofraxidin) were baseline separated within 5.3 min in samples, which represented an approximate six-fold reduction in the analysis time in comparison to published HPLC method. Quantitation was carried out working in the V mode using the narrow widow extracted ion chromatograms (nwXICs) of each compound (extracted using a 20 mDa window). Furthermore, all calibration curves showed good linearity (r > 0.999) within the test ranges. The precision was evaluated by intra- and inter-day tests, which revealed relative standard deviation (RSD) values of less than 3.88%. The recoveries for the quantified compounds were between 96.3% and 103.7%, with RSD values below 2.89%. According to the literature, this study represents the first investigation of the simultaneous analysis of multiple components and the method can be applied to determine the amounts of the major compounds in Acanthopanax senticosus and its extract by UPLC-TOF-MS. Full article

Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to ¹H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in ¹H NMR/RRLC–MS PDS spectrum, ¹H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. ¹H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds. Full article

Ionocovalency (IC), a quantitative dual nature of the atom, is defined and correlated with quantum-mechanical potential to describe quantitatively the dual properties of the bond. Orbiotal hybrid IC model scale, IC, and IC electronegativity scale, X_IC, are proposed, wherein the ionicity and the covalent radius are determined by spectroscopy. Being composed of the ionic function I and the covalent function C, the model describes quantitatively the dual properties of bond strengths, charge density and ionic potential. Based on the atomic electron configuration and the various quantum-mechanical built-up dual parameters, the model formed a Dual Method of the multiple-functional prediction, which has much more versatile and exceptional applications than traditional electronegativity scales and molecular properties. Hydrogen has unconventional values of IC and X_IC, lower than that of boron. The IC model can agree fairly well with the data of bond properties and satisfactorily explain chemical observations of elements throughout the Periodic Table. Full article