Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of a Short Peptide with G-Quadruplex-Forming Sequences: An SRCD and CD Study

G-quadruplex (G4) forming DNA sequences were recently found to play a crucial role in the regulation of genomic processes such as replication, transcription and translation, also related to serious diseases. Therefore, systems capable of controlling DNA and RNA G-quadruplex structures would be useful for the modulation of various cellular events. In particular, peptides represent good candidates for targeting G-quadruplex structures, since they are easily tailored to enhance their functionality. In this work, we analyzed, by circular dichroism and synchrotron radiation circular dichroism spectroscopies, the interaction of a 25-residue peptide deriving from RHAU helicases (Rhau25) with three G-quadruplex-forming oligonucleotide sequences, in both sodium- and potassium-containing buffers, the most relevant monovalent cations in physiological conditions. The peptide displayed greater affinity for the G4 sequences adopting a parallel structure. However, it showed the ability to also interact with antiparallel or hybrid G-quadruplex structures, inducing a conformation conversion to the parallel structure. The stability of the oligonucleotide structure alone or in presence of the Rhau25 peptide was studied by temperature melting and UV denaturation experiments, and the data showed that the interaction with the peptide stabilized the conformation of oligonucleotide sequences when subjected to stress conditions.
Dynamics of Polyphenol Biosynthesis by Calli Cultures, Suspension Cultures and Wild Specimens of the Medicinal Plant Ligaria cuneifolia (Ruiz & Pav.) Tiegh. (Loranthaceae). Analysis of Their Biological Activity

Ligaria cuneifolia (R. et P.) Tiegh. (Loranthaceae) is a South American hemiparasitic species with antioxidant, antitumoral, antimicrobial, and antilipidemic activities attributed to its polyphenolic content. We studied the polyphenolic pattern of L. cuneifolia during different phenological stages: flowering, fruiting, and post-fruiting. The highest total phenolic content was found in stems at post-fruiting (214 ± 12.1 mg gallic acid eq·g−1 DW) and fruiting (209 ± 13.7 mg gallic acid eq·g−1 DW), followed by post-fruiting leaves (207 ± 17.5 mg gallic acid eq·g−1 DW). Flavonoids accumulated at higher levels in leaves and hydroxycinnamic acids in leaves at flowering and post-fruiting. The polyphenolic pattern was similar between organs from wild plants and in vitro cultures, although at a significantly lower level in the latter ones. The performance of calli growing under a 16 h photoperiod in a modified White medium with 1-naphthalene acetic acid (2.50 μM) and Kinetin (9.20 μM) was better than in the dark. When calli grew in media only with auxins (IAA, NAA, and 2,4-D, all at 2.50 µM concentration), its growth and polyphenolic content improved. Cell suspensions with 2.50 µM NAA and 9.20 µM KIN grew slowly and produced very small amounts of polyphenols. As for the antioxidant activity, it was detected in all samples (approximately 1000 µmol trolox eq·g−1 DW) except fruits, where a lower value was found (328 µmol trolox eq·g−1 DW). In vitro cultures have the lowest antioxidant activity when compared to methanolic extracts from organs of wild specimens. Finally, antimutagenic or mutagenic activity in wild plants and in vitro culture extracts was not detected by the Ames test.
Stability of charges in titanium compounds and charge transfer to oxygen in titanium dioxide

We investigate the charge density distribution in titanium dioxide, molecular titanium complexes and a variety of periodic titanium compounds using delocalization indices and Bader charge analysis. Our results are in agreement with previous experimental and theoretical investigations on the charge stability and deviation from formal oxidation states in transition metal compounds. We present examples for practically relevant redox processes, using molecular titanium dioxide model systems, that illustrate the failure of formal oxidation states to account for some redox phenomena. We observe a pronounced charge stability on titanium for trial systems which are expected to be mainly ionic. No environment tested by us is capable to reduce the local titanium charge remainder below one electron.
Relationship between Latent Toxoplasmosis and Depression in Clients of a Center for Assisted Reproduction

Latent infection of the globally spread parasite Toxoplasma gondii in humans has been associated with changes in personality and behavior. Numerous studies have investigated the effect of toxoplasmosis on depression, but their results are inconsistent. Our study focused on the effect of latent toxoplasmosis on depression in men and women in association with their fertility. In 2016–2018, we recruited clients (677 men and 664 women) of the Center for Assisted Reproduction and asked them to complete a standardized Beck Depression Inventory-II. In women without fertility problems, we found higher depression scores in Toxoplasma-positive than in Toxoplasma-negative (p = 0.010, Cohen’s d = 0.48). Toxoplasma-positive infertile men, on the other hand, had lower depression scores than Toxoplasma-negative infertile men (p ≤ 0.001, Cohen’s d = 0.48). Our results are consistent with the previously described effects of latent toxoplasmosis, which seem to go in opposite directions regarding the effect on personality and behavior of men and women. Our results could be explained by gender-contrasting reactions to chronic stress associated with lifelong infection. This suggests that due to gender differences in the impact of latent toxoplasmosis, future studies ought to perform separate analyses for women and men.
Adaptive Immune Response to Vaccinia Virus LIVP Infection of BALB/c Mice and Protection against Lethal Reinfection with Cowpox Virus

Mass vaccination has played a critical role in the global eradication of smallpox. Various vaccinia virus (VACV) strains, whose origin has not been clearly documented in most cases, have been used as live vaccines in different countries. These VACV strains differed in pathogenicity towards various laboratory animals and in reactogenicity exhibited upon vaccination of humans. In this work, we studied the development of humoral and cellular immune responses in BALB/c mice inoculated intranasally (i.n.) or intradermally (i.d.) with the VACV LIVP strain at a dose of 105 PFU/mouse, which was used in Russia as the first generation smallpox vaccine. Active synthesis of VACV-specific IgM in the mice occurred on day 7 after inoculation, reached a maximum on day 14, and decreased by day 29. Synthesis of virus-specific IgG was detected only from day 14, and the level increased significantly by day 29 after infection of the mice. Immunization (i.n.) resulted in significantly higher production of VACV-specific antibodies compared to that upon i.d. inoculation of LIVP. There were no significant differences in the levels of the T cell response in mice after i.n. or i.d. VACV administration at any time point. The maximum level of VACV-specific T-cells was detected on day 14. By day 29 of the experiment, the level of VACV-specific T-lymphocytes in the spleen of mice significantly decreased for both immunization procedures. On day 30 after immunization with LIVP, mice were infected with the cowpox virus at a dose of 46 LD50. The i.n. immunized mice were resistant to this infection, while 33% of i.d. immunized mice died. Our findings indicate that the level of the humoral immune response to vaccination may play a decisive role in protection of animals from orthopoxvirus reinfection.
Molecular Characterization of Human Papillomavirus Type 159 (HPV159)

Human papillomavirus type 159 (HPV159) was identified in an anal swab sample and preliminarily genetically characterized by our group in 2012. Here we present a detailed molecular in silico analysis that showed that the HPV159 viral genome is 7443 bp in length and divided into five early and two late genes, with conserved functional domains and motifs, and a non-coding long control region (LCR) with significant regulatory sequences that allow the virus to complete its life cycle and infect novel host cells. HPV159, clustering into the cutaneotropic Betapapillomavirus (Beta-PV) genus, is phylogenetically most similar to HPV9, forming an individual phylogenetic group in the viral species Beta-2. After testing a large representative collection of clinical samples with HPV159 type-specific RT-PCR, in addition to the anal canal from which the first HPV159 isolate was obtained, HPV159 was further detected in other muco-cutaneous (4/181, 2.2%), mucosal (22/764, 2.9%), and cutaneous (14/554, 2.5%) clinical samples, suggesting its extensive tissue tropism. However, because very low HPV159 viral loads were estimated in the majority of positive samples, it seemed that HPV159 mainly caused clinically insignificant infections of the skin and mucosa. Using newly developed, highly sensitive HPV159-specific nested PCRs, two additional HPV159 LCR viral variants were identified. Nevertheless, all HPV159 mutations were demonstrated outside important functional domains of the LCR, suggesting that the HPV159 viral variants were most probably not pathogenically different. This complete molecular characterization of HPV159 enhances our knowledge of the genome characteristics, tissue tropism, and phylogenetic diversity of Beta-PVs that infect humans.
Limited HIV-1 Subtype C nef 3′PPT Variation in Combination Antiretroviral Therapy Naïve and Experienced People Living with HIV in Botswana

Dolutegravir (DTG) is a potent anti-HIV drug that is used to treat HIV globally. There have been reports of mutations in the HIV-1 3′-polypurine tract (3′PPT) of the nef gene, contributing to DTG failure; however, there are limited ‘real-world’ data on this. In addition, there is a knowledge gap on the variability of 3′PPT residues in patients receiving combination antiretroviral therapy (cART) with and without viral load (VL) suppression. HIV-1 subtype C (HIV-1C) whole-genome sequences from cART naïve and experienced individuals were generated using next-generation sequencing. The nef gene sequences were trimmed from the generated whole-genome sequences using standard bioinformatics tools. In addition, we generated separate integrase and nef gene sequences by Sanger sequencing of plasma samples from individuals with virologic failure (VF) while on a DTG/raltegravir (RAL)-based cART. Analysis of 3′PPT residues was performed, and comparison of proportions computed using Pearson’s chi-square test with p-values < 0.05 was considered statistically significant. A total of 6009 HIV-1C full genome sequences were generated and had a median log10 HIV-1 VL (Q1, Q3) copies/mL of 1.60 (1.60, 2.60). A total of 12 matching integrase and nef gene sequences from therapy-experienced participants failing DTG/ RAL-based cART were generated. HIV-1C 3′PPT nef gene sequences from therapy-experienced patients failing DTG cART (n = 12), cART naïve individuals (n = 1263), and individuals on cART with and without virological suppression (n = 4696) all had a highly conserved 3′PPT motif with no statistically significant differences identified. Our study confirms the high conservation of the HIV-1 nef gene 3′PPT motif in ‘real-world’ patients and showed no differences in the motif according to VL suppression or INSTI-based cART failure. Future studies should explore other HIV-1 regions outside of the pol gene for associations with DTG failure.
Nervous and Muscular Adverse Events after COVID-19 Vaccination: A Systematic Review and Meta-Analysis of Clinical Trials

Background: Nervous and muscular adverse events (NMAEs) have garnered considerable attention after the vaccination against coronavirus disease (COVID-19). However, the incidences of NMAEs remain unclear. We aimed to calculate the pooled event rate of NMAEs after COVID-19 vaccination. Methods: A systematic review and meta-analysis of clinical trials on the incidences of NMAEs after COVID-19 vaccination was conducted. The PubMed, Medline, Embase, Cochrane Library, and Chinese National Knowledge Infrastructure databases were searched from inception to 2 June 2021. Two independent reviewers selected the study and extracted the data. Categorical variables were analyzed using Pearson’s chi-square test. The pooled odds ratio (OR) with the corresponding 95% confidence intervals (CIs) were estimated and generated with random or fixed effects models. The protocol of the present study was registered on PROSPERO (CRD42021240450). Results: In 15 phase 1/2 trials, NMAEs occurred in 29.2% vs. 21.6% (p < 0.001) vaccinated participants and controls. Headache and myalgia accounted for 98.2% and 97.7%, and their incidences were 16.4% vs. 13.9% (OR = 1.97, 95% CI = 1.28–3.06, p = 0.002) and 16.0% vs. 7.9% (OR = 3.31, 95% CI = 2.05–5.35, p < 0.001) in the vaccine and control groups, respectively. Headache and myalgia were more frequent in the newly licensed vaccines (OR = 1.97, 95% CI = 1.28–3.06, p = 0.02 and OR = 3.31, 95% CI = 2.05–5.35, p < 0.001) and younger adults (OR = 1.40, 95% CI = 1.12–1.75, p = 0.003 and OR = 1.54, 95% CI = 1.20–1.96, p < 0.001). In four open-label trials, the incidences of headache, myalgia, and unsolicited NMAEs were 38.7%, 27.4%, and 1.5%. Following vaccination in phase 3 trials, headache and myalgia were still common with a rate of 29.5% and 19.2%, although the unsolicited NMAEs with incidence rates of ≤ 0.7% were not different from the control group in each study. Conclusions: Following the vaccination, NMAEs are common of which headache and myalgia comprised a considerable measure, although life-threatening unsolicited events are rare. NMAEs should be continuously monitored during the ongoing global COVID-19 vaccination program.
Meta-analysis of the efficacy of Da Vinci robotic or laparoscopic distal subtotal gastrectomy in patients with gastric cancer

Abstract Background: Robotic-assisted gastrectomy has been used for treating gastric cancer since 2002. This meta-analysis was conducted to systematically evaluate the efficacy of Da Vinci robotic distal subtotal gastrectomy (RDG) or laparoscopic distal subtotal gastrectomy (LDG) in patients with gastric cancer. Methods: We conducted searches in domestic and foreign databases, and collected literature in Chinese and English on the efficacy of RDG and LDG for gastric cancer that have been published since the inception of the database. RevMan 5.4. 1 was used for meta-analysis and drawing and Stata14.0 was used for publication bias analysis. Results: A total of 3293 patients in 15 studies were included, including 1193 patients in the RDG group and 2100 patients in the LDG groups respectively. The meta-analysis showed that intraoperative blood loss was significantly lower and the number of resected lymph nodes was higher in the RDG group compared to that in the LDG group. In addition, the times to first postoperative food intake and postoperative hospital stay were shortened, and there was a longer length of distal resection margin and prolonged duration of operation. No significant differences were found between the 2 groups with respect to the first postoperative anal exhaust time, length of proximal resection margin, total postoperative complication rate, postoperative anastomotic leakage rate, incidence of postoperative gastric emptying disorder, pancreatic fistula rate, recurrence rate, and mortality rate. Conclusion: RDG is a safe and feasible treatment option for gastric cancer, and it is non-inferior or even superior to LDG with respect to therapeutic efficacy and radical treatment.
Membrane Emulsification Process as a Method for Obtaining Molecularly Imprinted Polymers

The membrane emulsification process (ME) using a metallic membrane was the first stage for preparing a spherical and monodisperse thermoresponsive molecularly imprinted polymer (TSMIP). In the second step of the preparation, after the ME process, the emulsion of monomers was then polymerized. Additionally, the synthesized TSMIP was fabricated using as a functional monomer N-isopropylacrylamide, which is thermosensitive. This special type of polymer was obtained for the recognition and determination of trace bisphenol A (BPA) in aqueous media. Two types of molecularly imprinted polymers (MIPs) were synthesized using amounts of BPA of 5 wt. % (MIP-2) and 7 wt. % (MIP-1) in the reaction mixtures. Additionally, a non-imprinted polymer (NIP) was also synthesized. Polymer MIP-2 showed thermocontrolled recognition for imprinted molecules and a higher binding capacity than its corresponding non-imprinted polymer and higher than other molecularly imprinted polymer (MIP-1). The best condition for the sorption process was at a temperature of 35 °C, that is, at a temperature close to the phase transition value for poly(N-isopropylacrylamide). Under these conditions, the highest levels of BPA removal from water were achieved and the highest adsorption capacity of MIP-2 was about 0.5 mmol g−1 (about 114.1 mg g−1) and was approximately 20% higher than for MIP-1 and NIP. It was also observed that during the kinetic studies, under these temperature conditions, MIP-2 sorbed BPA faster and with greater efficiency than its non-imprinted analogue.
Incorporating Interpersonal Synchronization Features for Automatic Emotion Recognition from Visual and Audio Data during Communication

During social interaction, humans recognize others’ emotions via individual features and interpersonal features. However, most previous automatic emotion recognition techniques only used individual features—they have not tested the importance of interpersonal features. In the present study, we asked whether interpersonal features, especially time-lagged synchronization features, are beneficial to the performance of automatic emotion recognition techniques. We explored this question in the main experiment (speaker-dependent emotion recognition) and supplementary experiment (speaker-independent emotion recognition) by building an individual framework and interpersonal framework in visual, audio, and cross-modality, respectively. Our main experiment results showed that the interpersonal framework outperformed the individual framework in every modality. Our supplementary experiment showed—even for unknown communication pairs—that the interpersonal framework led to a better performance. Therefore, we concluded that interpersonal features are useful to boost the performance of automatic emotion recognition tasks. We hope to raise attention to interpersonal features in this study.
Contribution of Visible Surface Mold to Airborne Fungal Concentration as Assessed by Digital Image Quantification

The rapid monitoring of total fungi, including air and surface fungal profiling, is an important issue. Here, we applied air and surface sampling, combined with digital image quantification of surface mold spots, to evaluate the contribution of surface fungi to airborne fungal concentrations. Cladosporium, Penicillium, Aspergillus, and yeast often appeared in the air or on wall surfaces during sampling. The indoor/outdoor concentration ratios (I/O ratios) demonstrated that the airborne concentrations of commonly found fungal genera outdoors were higher than those indoors (median I/O ratio = 0.65–0.91), excluding those of Penicillium and yeast. Additionally, the surface density (fungal concentration/area) of individual fungi showed no significant correlation with the airborne concentration, excluding that of Geotrichum. However, if a higher surface ratio (>0.00031) of mold spots appeared in the total area of an indoor environment, then the concentrations of Aspergillus and Geotrichum in the air increased significantly. Our results demonstrated that the airborne concentration of indoor fungi is significantly correlated with the outdoor concentration. A higher density of surface fungi does not necessarily contribute to a high fungal concentration in the air. In contrast to fungal density, quantification of the surface fungal area is recommended to assess the risk of surface fungi propelling into the air.
Longitudinal Assessment of Cytokine Expression and Plasminogen Activation in Hantavirus Cardiopulmonary Syndrome Reveals Immune Regulatory Dysfunction in End-Stage Disease

Pathogenic New World orthohantaviruses cause hantavirus cardiopulmonary syndrome (HCPS), a severe immunopathogenic disease in humans manifested by pulmonary edema and respiratory distress, with case fatality rates approaching 40%. High levels of inflammatory mediators are present in the lungs and systemic circulation of HCPS patients. Previous studies have provided insights into the pathophysiology of HCPS. However, the longitudinal correlations of innate and adaptive immune responses and disease outcomes remain unresolved. This study analyzed serial immune responses in 13 HCPS cases due to Sin Nombre orthohantavirus (SNV), with 11 severe cases requiring extracorporeal membrane oxygenation (ECMO) treatment and two mild cases. We measured viral load, levels of various cytokines, urokinase plasminogen activator (uPA), and plasminogen activator inhibitor-1 (PAI-1). We found significantly elevated levels of proinflammatory cytokines and PAI-1 in five end-stage cases. There was no difference between the expression of active uPA in survivors’ and decedents’ cases. However, total uPA in decedents’ cases was significantly higher compared to survivors’. In some end-stage cases, uPA was refractory to PAI-1 inhibition as measured by zymography, where uPA and PAI-1 were strongly correlated to lymphocyte counts and IFN-γ. We also found bacterial co-infection influencing the etiology and outcome of immune response in two cases. Unsupervised Principal Component Analysis and hierarchical cluster analyses resolved separate waves of correlated immune mediators expressed in one case patient due to a sequential co-infection of bacteria and SNV. Overall, a robust proinflammatory immune response, characterized by an imbalance in T helper 17 (Th17) and regulatory T-cells (Treg) subsets, was correlated with dysregulated inflammation and mortality. Our sample size is small; however, the core differences correlated to survivors and end-stage HCPS are instructive.
Clinical utiliy of a model‐based piperacillin dose in neonates with early‐onset sepsis

Early‐onset sepsis (EOS) is a common disease in neonates with a high morbidity and mortality rate. Piperacillin/tazobactam has been used extensively and empirically for EOS treatment without clinically validated dosing regimens, although the population pharmacokinetics (PPK) of piperacillin in neonates has been reported. Therefore, we wanted to study the effectiveness and tolerance of a PPK model‐based dosing regimen of piperacillin/tazobactam in EOS patients.