Miracle-dz/UniFAR-FTUs huggingface dataset:
Theoretical studies on the structure and dynamics of room-temperature ionic liquids

In this thesis, we present our studies on the structure and dynamics of novel Room-Temperature Ionic Liquids. Through our computer simulations we demonstrate that the kinetics of photo induced electron transfer reaction between S1 and S2 states of Crystal Violet Lactone in N-propyl-N-methylpyrrolidiniumbis(trifluoromethylsulfonyl)imide([Pr31][NTf2]) room temperature ionic liquid is local solvent environment dependent, because emission time scales are smaller than solvent relaxation time scales. This behavior is characteristic of ionic liquids but uncommon in conventional solvents. Therefore ionic liquids open a window of opportunity for manipulating the outcome of chemical reactions simply by tuning the initial excitation wavelength. We performed Molecular dynamics simulations of mixtures of 1-hexyl-3-methyl imidazoliumhexafluorophosphate ([C6MIM][PF6 ] ) and water in order to investigate how small amounts of water affect the translational and rotational dynamics of ionic liquids. We find that water is closely associated with the anions and that its presence enhances both the translational and rotational dynamics of the ionic liquid. In agreement with experiments, we find that the fluorescence spectra of Coumarin-153 is red-shifted because of the presence of water. Small amounts of water enhance the speed of relaxation of the solvent surrounding the solute probe after photo-excitation, but only at a local environment level. Interconversion between environments still occurs on a long time scale compared with the fluorescence lifetime of the probe. To interpret the features of x-ray scattering structure factor of room temper-
Quantification of Proteins Involved in Intestinal Epithelial Handling of Xenobiotics

The intestinal epithelium represents a natural barrier against harmful xenobiotics, while facilitating the uptake of nutrients and other substances. Understanding the interaction of chemicals with constituents of the intestinal epithelium and their fate in the body requires quantitative measurement of relevant proteins in in vitro systems and intestinal epithelium. Recent studies have highlighted the mismatch between messenger RNA (mRNA) and protein abundance for several drug‐metabolizing enzymes and transporters in the highly dynamic environment of the intestinal epithelium; mRNA abundances cannot therefore be used as a proxy for protein abundances in the gut, necessitating direct measurements. The objective was to determine the expression of a wide range proteins pertinent to metabolism and disposition of chemicals and nutrients in the intestinal epithelium. Ileum and jejunum biopsy specimens were obtained from 16 patients undergoing gastrointestinal elective surgery. Mucosal fractions were prepared and analyzed using targeted and global proteomic approaches. A total of 29 enzymes, 32 transporters, 6 tight junction proteins, 2 adhesion proteins, 1 alkaline phosphatase, 1 thioredoxin, 5 markers, and 1 regulatory protein were quantified—60 for the first time. The global proteomic method identified a further 5,222 proteins, which are retained as an open database for interested parties to explore. This study significantly expands our knowledge of a wide array of proteins important for xenobiotic handling in the intestinal epithelium. Quantitative systems biology models will benefit from the novel systems data generated in the present study and the translation path offered for in vitro to in vivo translation.
Mold-Face Heating Mechanism, Overflow-Well Design, and Their Effect on Surface Weldline and Tensile Strength of Long-Glass-Fiber-Reinforced Polypropylene Injection Molding

Long-fiber polymers offer the advantage of a lower production cost because specific tool designs are required for conventional injection molding equipment to produce long-fiber polymer parts. The use of long fibers allows relatively high fiber aspect ratios to be obtained, thereby enhancing composite stiffness, strength, creep endurance, and fatigue endurance. However, the multigate design of the injection-molded part can result in weldline formation during the molding process, which reduces the structural strength of the molded part. Therefore, in this study, the surface quality, fiber compatibility, and structural strength of long-glass-fiber-reinforced polypropylene (PP/LGF) injection-molded samples were compared in the use versus nonuse of a mold-cavity overflow-well area and the mold-face infrared heating method. The experimental results indicate that the mold-cavity overflow-well area more greatly improved the surface roughness of the PP/LGF molded samples. Moreover, the infrared heating of the mold-face decreased the weldline depth of the samples. Optical-microscopy images and mold-cavity pressure distributions indicated that the weldline tensile strength and the interface compatibility between fibers and melts at the weldline region during the molding stage were higher in the use than in the nonuse of the mold-cavity overflow-well and mold-face infrared heating method.
Latin American Genes: The Great Forgotten in Rheumatoid Arthritis

The successful implementation of personalized medicine will rely on the integration of information obtained at the level of populations with the specific biological, genetic, and clinical characteristics of an individual. However, because genome-wide association studies tend to focus on populations of European descent, there is a wide gap to bridge between Caucasian and non-Caucasian populations before personalized medicine can be fully implemented, and rheumatoid arthritis (RA) is not an exception. In this review, we discuss advances in our understanding of genetic determinants of RA risk among global populations, with a focus on the Latin American population. Geographically restricted genetic diversity may have important implications for health and disease that will remain unknown until genetic association studies have been extended to include Latin American and other currently under-represented ancestries. The next few years will witness many breakthroughs in personalized medicine, including applications for common diseases and risk stratification instruments for targeted prevention/intervention strategies. Not all of these applications may be extrapolated from the Caucasian experience to Latin American or other under-represented populations.
Impact of Feature Selection Algorithm on Speech Emotion Recognition Using Deep Convolutional Neural Network

Speech emotion recognition (SER) plays a significant role in human–machine interaction. Emotion recognition from speech and its precise classification is a challenging task because a machine is unable to understand its context. For an accurate emotion classification, emotionally relevant features must be extracted from the speech data. Traditionally, handcrafted features were used for emotional classification from speech signals; however, they are not efficient enough to accurately depict the emotional states of the speaker. In this study, the benefits of a deep convolutional neural network (DCNN) for SER are explored. For this purpose, a pretrained network is used to extract features from state-of-the-art speech emotional datasets. Subsequently, a correlation-based feature selection technique is applied to the extracted features to select the most appropriate and discriminative features for SER. For the classification of emotions, we utilize support vector machines, random forests, the k-nearest neighbors algorithm, and neural network classifiers. Experiments are performed for speaker-dependent and speaker-independent SER using four publicly available datasets: the Berlin Dataset of Emotional Speech (Emo-DB), Surrey Audio Visual Expressed Emotion (SAVEE), Interactive Emotional Dyadic Motion Capture (IEMOCAP), and the Ryerson Audio Visual Dataset of Emotional Speech and Song (RAVDESS). Our proposed method achieves an accuracy of 95.10% for Emo-DB, 82.10% for SAVEE, 83.80% for IEMOCAP, and 81.30% for RAVDESS, for speaker-dependent SER experiments. Moreover, our method yields the best results for speaker-independent SER with existing handcrafted features-based SER approaches.
The Prevalence of Gastrointestinal Symptoms, Abnormal Liver Function, Digestive System Disease and Liver Disease in COVID-19 Infection

Supplemental Digital Content is available in the text. Background: The worldwide outbreak of COVID-19 infected millions of people. Some patients had gastrointestinal (GI) symptoms, abnormal liver function, digestive system disease and liver disease. Aim: To investigate the prevalence of GI symptoms, abnormal liver function, digestive system disease and liver disease in patients with COVID-19 by a systematic review and meta-analysis. Methods: We searched PubMed, Ovid Embase, Medline, and 2 Chinese databases. Primary outcomes were the prevalence of GI symptoms, abnormal liver function, digestive system disease, and liver disease. Different studies were included in different subset analysis. These outcomes were estimated with proportions, odds ratio, 95% confidence interval (CI) and P-value by Stata SE 15.1. Results: Thirty-one studies involving 4682 patients were included. The most significant GI symptoms were diarrhea (0.08, 95% CI: 0.06-0.11) and anorexia (0.17, 95% CI: 0.06-0.27). The most significant abnormal liver function was increased alanine aminotransferase (ALT) (0.25, 95% CI: 0.16-0.33). A total of 5% of the patients had digestive system disease (95% CI: 0.02-0.08). A total of 3% of the patients had liver disease (95% CI: 0.02-0.05). The prevalence of nausea and vomiting, diarrhea, abnormal liver function, digestive system disease, and liver disease was higher in Wuhan group. The prevalence of diarrhea was higher in non-China group. Patients in severe/intensive care unit group were more likely to have diarrhea, anorexia, abdominal pain increased aspartate aminotransferase, and increased ALT. Conclusion: The most significant GI symptoms were anorexia and diarrhea. The most significant abnormal liver function was increased ALT. Severe patients were more likely to have GI symptoms and abnormal liver function.
Development of integrated multi-trophic aquaculture (IMTA) for tropical brackishwater species in Sindhudurg District, Maharashtra, west coast of India

Integrated multi-trophic aquaculture (IMTA), farming of species from different trophic levels and with complimentary ecosystem function, is regarded as a suitable approach to develop a sustainable aquaculture system. In order to establish an IMTA system, a study was carried out in Sindhudurg District, Maharashtra, India for selected tropical brackish-water species. Two equal sized pens (250 m2) were constructed for IMTA and control respectively in each land based system and open water cages were set in the estuary. Different combinations of fed species (Chanos chanos, Etroplus suratensis, Mugil cephalus, Penaeus indicus) and an extractive crop (Crassostrea madrasensis) were stocked in IMTA experimental system whereas monoculture of P. indicus served as control. Water quality characteristics were found to be within the admissible limits. Soil organic carbon was found to be lesser in the IMTA system compared to control. The productivity of IMTA system was higher than control: 3250 kg h-1 vs 2000 kg ha-1. Further, income and benefit-cost ratio was found to be higher in IMTA pens. The present study concludes that IMTA is a possible option for system diversification as well as species diversification without compromising economic profitability of culture.
The Autonomous Landing of Rotary-Wing UAVs on Underway Ships in a Sea State

ix List of Abbreviations and Symbols Used . x Acknowledgements . xiii Chapter
The influence of mild versus severe hypodontia on facial soft tissues? A three-dimensional optical laser scanning-based cohort study

Objective: To determine whether there are differences in the facial soft tissue morphology between participants with mild (up to two) or severe (six or more) hypodontia. Design and Setting: A prospective hospital-based cohort study. Participants and Methods: Ninety-two participants, aged 11–16 years, with confirmed hypodontia were recruited. Participants were sub-grouped based on the severity (mild, two or less and severe, six or more) and distribution of the missing teeth and age. They underwent a three-dimensional (3D) optical surface scan of the facial soft tissues. Facial surface scans were compared quantitatively, applying landmark measurements and surface-based analysis. Results: In total, 92 participants, with an equal distribution between the mild (n=46) and severe (n=46) categories, were recruited. Patients with severe hypodontia displayed a reduced alar base, lower facial height, nasolabial angle (P = 0.02) and transgonial width (P < 0.001) compared to those with milder hypodontia. Furthermore, significant differences were observed between mild-male and severe-female groups regarding alar base, lower anterior face height and transgonial width and between mild-male and mild-female groups regarding nasolabial angle and transgonial width. Conclusion: Significant reductions were seen in the 3D soft tissue morphology of participants with severe hypodontia, in terms of the nasolabial angle, lower facial height, alar base and transgonial widths, emphasising the importance of using facial scanning as a relatively simple non-invasive method of assessment.
Relationships between changes in self-reported physical activity, sedentary behaviour and health during the coronavirus (COVID-19) pandemic in France and Switzerland

ABSTRACT To assess whether changes in physical activity and sedentary behaviour during the COVID-19 lockdown are associated with changes in mental and physical health. Observational longitudinal study. Participants living in France or Switzerland responded to online questionnaires measuring physical activity, physical and mental health, anxiety, and depressive symptoms. Paired sample t-tests were used to assess differences in physical activity and sedentary behaviour before and during lockdown. Multiple linear regressions were used to investigate associations between changes in physical activity and changes in mental and physical health during lockdown. 267 (wave1) and 110 participants (wave2; 2 weeks later) were recruited. Lockdown resulted in higher time spent in walking and moderate physical activity (~10min/day) and in sedentary behaviour (~75min/day), compared to pre COVID-19. Increased physical activity during leisure time from week 2 to week 4 of lockdown was associated with improved physical health (β=.24, p=.002). Additionally, an increase in sedentary behaviour during leisure time was associated with poorer physical health (β=−.35, p=.002), mental health (β=−.25, p=.003), and subjective vitality (β=−.30, p=.004). Ensuring sufficient levels of physical activity and reducing sedentary time can play a vital role in helping people to cope with a major stressful event, such as the COVID-19 pandemic.
“Walking on Eggshells:” A Qualitative Study of How Friends of Young Women Experiencing Intimate Partner Violence Perceive Their Role

Young women who experience intimate partner violence (IPV) are most likely to turn to their friends for help. Although friends can play a critical role in providing support, there is little research that examines friends’ experiences. In this qualitative study, we explored how friends of young women experiencing IPV perceived their role in responding to IPV in the context of friendship. We held in-depth interviews with 15 friends of young women who had experienced IPV and used reflexive thematic analysis to develop key themes from the data. We developed two overarching themes that reflected participants’ perceptions of the roles they had played or considered as a friend in responding to IPV: “taking action” (which included “providing an outsider’s view,” “being an advisor or coach,” “being a protector,” and “taking a stand”); and “being there” (which included “being a listener,” “being a companion” and “being an ally”). Their perceptions were shaped by friendship expectations, as well as by understandings of IPV. However, deciding what role to play in supporting their friend was constructed as challenging due to conflicting expectations that arose in the context of friendship. It involved balancing a perceived responsibility to do what they thought was best for their friend’s well-being, a need to promote honesty and mutuality in the friendship, along with a competing obligation to respect their friend’s choices, maintain her trust and ensure equality in the friendship. Being friends with the abuser as well as with the victim created additional complexities. Based on our findings, we identify key areas to address in developing interventions to assist friends to respond to young women experiencing IPV. These could guide friends on how to play an effective support role while also maintaining the friendship and managing the significant emotional impacts of providing help.
Evaluation of the Association between Programmed Cell Death-1 Gene Polymorphisms and Hepatocellular Carcinoma Susceptibility in Turkish Subjects. A Pilot Study.

BACKGROUND AND AIMS Programmed cell death-1 (PD-1) has a vital role in regulating T-cell function, and immune escape mechanism of cancer cells. It was shown that there could be a relationship between single nucleotide polymorphisms (SNPs) in the PD-1 gene and susceptibility to hepatocellular carcinoma (HCC) based on various studies. We aimed to investigate the role of three SNPs within the PD-1 gene in susceptibility to HCC in the Turkish population. METHODS Single nucleotide polymorphisms of PD-1.1, 1.5, and 1.6 were genotyped by using TaqMan Allelic Discrimination Assays in blood samples of 137 HCC and 136 control subjects, matched for age and gender. The genotype, allele and haplotype frequencies were compared in HCC and control groups using logistic regression analysis. RESULTS Genotype distributions of PD-1.1, PD-1.5 and PD-1.6 SNPs were in Hardy-Weinberg equilibrium. No significant difference was observed in the genotype distribution of PD-1.1, PD-1.5 and PD-1.6 polymorphisms among gender and age-matched HCC (M/F: 96/41; mean age: 61.4 ±11.7 years) and control group (M/F: 94/42; mean age: 61.4±10.1). In the haplotype analysis of PD-1.1/PD-1.5/PD-1.6, no significant difference was found among HCC and control group adjusted for sex and age (all p values>0.1). CONCLUSION Our findings, firstly reporting the association of PD-1.5 polymorphism with HCC, and PD-1.1 and PD-1.6 with HCC in the Turkish population, suggest that PD-1 polymorphisms are not predisposing factors for HCC development. Future studies with larger sample sizes and different ethnic populations are required to validate our findings.
Efflux Pump-Driven Antibiotic and Biocide Cross-Resistance in Pseudomonas aeruginosa Isolated from Different Ecological Niches: A Case Study in the Development of Multidrug Resistance in Environmental Hotspots

Pseudomonas aeruginosa is an opportunistic pathogen displaying high intrinsic antimicrobial resistance and the ability to thrive in different ecological environments. In this study, the ability of P. aeruginosa to develop simultaneous resistance to multiple antibiotics and disinfectants in different natural niches were investigated using strains collected from clinical samples, veterinary samples, and wastewater. The correlation between biocide and antimicrobial resistance was determined by employing principal component analysis. Molecular mechanisms linking biocide and antimicrobial resistance were interrogated by determining gene expression using RT-qPCR and identifying a potential genetic determinant for co- and cross-resistance using whole-genome sequencing. A subpopulation of P. aeruginosa isolates belonging to three sequence types was resistant against the common preservative benzalkonium chloride and showed cross-resistance to fluoroquinolones, cephalosporins, aminoglycosides, and multidrug resistance. Of these, the epidemiological high-risk ST235 clone was the most abundant. The overexpression of the MexAB-OprM drug efflux pump resulting from amino acid mutations in regulators MexR, NalC, or NalD was the major contributing factor for cross-resistance that could be reversed by an efflux pump inhibitor. This is the first comparison of antibiotic-biocide cross-resistance in samples isolated from different ecological niches and serves as a confirmation of laboratory-based studies on biocide adapted isolates. The isolates from wastewater had a higher incidence of multidrug resistance and biocide-antibiotic cross-resistance than those from clinical and veterinary settings.
CyclinA1 Promoter Methylation in Self-Sampling Test

Background: Self sampled HPV testing is a cervical cancer screening method . However, cytology in self-sampled specimen cannot be used as a triage test. Therefore, other methods for triage should be considered. CyclinA1 (CCNA1) promoter methylation has strong association with cervical precancerous and cancerous lesion. The objective of this study was to compare the diagnostic value of CCNA1 and self-sampled specimen for detecting high-grade cervical intraepithelial lesions or worse (CIN2+). Materials and Methods: A cross sectional study was conducted. Women with abnormal cytology or positive for high risk HPV (hrHPV) indicated for colposcopic examination were enrolled. Self-collected sampling for hrHPV DNA (SS-HPV) and CCNA1 were performed. hrHPV DNA testing was done by Cobas 4800 method. CCNA1 promoter methylation was detected by CCNA1 duplex methylation specific PCR. Histopathologic result as CIN2+ obtaining from colposcopic directed biopsy or excisional procedure was considered as positive a gold standard. The results of hrHPV and CCNA1 were reported as positive or negative. Sensitivity specificity, positive predictive value, and negative predictive value of SS-HPV and CCNA1 were calculated by comparing the results with the gold standard. Results: Two hundreds and eighty women were recruited. High-grade cervical lesions and cervical cancer (CIN2+) were diagnosed in 21.8% (61 cases) of the patients. The most common type of hrHPV was non 16, 18 subtype, followed by HPV16 and 18. CCNA1 was positive in 13 patients out of whom, twelve were CIN2+. Sensitivity of CCNA1 was 19.7 % and its specificity and accuracy were 99.5% and 82.14%, respectively. The sensitivity of SS-HPV was 70.5%, and its specificity and accuracy were 39.2% and 43.3%, respectively. Conclusion: Due to high specificity and positive predictive value of CCNA1, it can be used as alarming sign of having high-grade cervical intraepithelial lesions, especially in patient who has positive hrHPV DNA test based on self-collected sampling.
Variability of salivary metabolite levels in patients with Sjögren's syndrome.

PURPOSE To investigate inter- and intra-individual variation in the levels and outputs (concentration multiplied by salivary flow rate) of salivary metabolites in patients with primary Sjögren's syndrome (pSS). METHODS A total of 56 samples of stimulated saliva were collected from 14 female pSS patients during four laboratory visits within 20 weeks and analyzed using proton nuclear magnetic resonance spectroscopy. Single saliva samples from each of 15 controls were also analyzed. RESULTS Among 21 quantified metabolites, choline was significantly elevated in the pSS patients at each time point (P ≤ 0.015), taurine at the last three time points (P ≤ 0.013), alanine at the last two time points (P ≤ 0.007) and glycine at the last time point (P = 0.005). Inter-individual variation in metabolite concentrations was generally larger among the patients than among the controls, and significantly large variations were observed for glycine (P ≤ 0.007, all time points), choline (P ≤ 0.033, three last time points) and alanine (P = 0.028, baseline). Metabolite output analysis showed that choline had the lowest intra-patient variation. CONCLUSION In spite of considerable intra- and inter-individual variation, levels and outputs of specific metabolites in patients with pSS differ from those in controls, and may be potentially applicable as new biological markers for monitoring of the response to treatment.