Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Genomics Identified PenR E151V Substitution Associated with Carbapenem-Resistance Burkholderia cepacia Complex and a Novel Burkholderia cepacia Complex Specific OXA-1043 Subgroup

Purpose Burkholderia cepacia complex (Bcc) is a known significant opportunistic pathogen causing morbidity and mortality, particularly in those with cystic fibrosis, chronic granulomatous disease, or immunocompromising host. Mortality of Bcc bloodstream infections among non-cystic fibrosis patients remained high. The antibiotic treatment for Bcc infection is quite challenging due to its intrinsic resistance to most antibiotics, and the resistance to carbapenems was the biggest concern among them. We aimed to realize the mechanism of carbapenem resistance in Bcc. Patients and Methods Ten strains of Bcc were identified by the MALDI-TOF MS, and the drug susceptibility test was using VITEK 2 system. The Burkholderia cepacia complex genomes were sequenced via Nanopore GridIon. We also downloaded another ninety-five strains of Bcc from the National Center for Biotechnology Information database to evaluate the divergence between carbapenem-resistance and carbapenem-sensitive strains. Results The genetic organization between carbapenem-sensitive and carbapenem-resistant strains of Bcc showed no difference. However, in the carbapenem-sensitive strain, E151V substitution in PenR was detected. In addition, a novel specific OXA family subgroup, blaOXA-1043 in Burkholderia cenocepacia was discovered. Conclusion The E151V substitution in PenR may be associated with carbapenem-sensitive in Bcc. Moreover, the V151E mutation in PenR may be related to the activation of PenB, leading to Bcc resistance to carbapenems. Besides, a novel OXA family subgroup, blaOXA-1043, was found in Burkholderia cenocepacia, which differs from the previous OXA family.
Electroanatomical Conduction Characteristics of Pig Myocardial Tissue Derived from High-Density Mapping

Background: Ultra-high-density mapping systems allow more precise measurement of the heart chambers at corresponding conduction velocities (CVs) and voltage amplitudes (VAs). Our aim for this study was to define and compare a basic value set for unipolar CV and VA in all four heart chambers and their separate walls in healthy, juvenile porcine hearts using ultra-high-density mapping. Methods: We used the Rhythmia Mapping System to create electroanatomical maps of four pig hearts in sinus rhythm. CVs and VAs were calculated for chambers and wall segments with overlapping circular areas (radius of 5 mm). Results: We analysed 21 maps with a resolution of 1.4 points/mm2. CVs were highest in the left atrium (LA), followed by the left ventricle (LV), right ventricle (RV), and right atrium (RA). As for VA, LV was highest, followed by RV, LA, and RA. The left chambers had a higher overall CV and VA than the right. Within the chambers, CV varied more in the right than in the left chambers, and VA varied in the ventricles but not in the atria. There was a slightly positive correlation between CVs and VAs at velocity values of <1.5 m/s. Conclusions: In healthy porcine hearts, the left chambers showed higher VAs and CVs than the right. CV differs mainly within the right chambers and VA differs only within the ventricles. A slightly positive linear correlation was found between slow CVs and low VAs.
Molecular Profiling, Characterization and Antimicrobial Efficacy of Silver Nanoparticles Synthesized from Calvatia gigantea and Mycena leaiana against Multidrug-Resistant Pathogens

The use of natural products isolated from mushrooms against infection, cancer diseases and other oxidative-stress-related diseases is one of the cornerstones of modern medicine. Therefore, we tried to establish a combination of medicinal mushrooms and nanotechnology possibly with the field of medicine for the development of antibacterial agents against these MDR strains. The aim of the research was to understand the molecular identification, characterization and antibacterial action of Calvatia gigantea and Mycena leaiana. The identification of fruiting body species via morpho-anatomical and molecular methods was necessary to analyze the genetic variability and phylogenetic relationships of mushrooms. Phylogenetic analysis revealed that Calvatia from Hunza, Pakistan, exhibited 98% resemblance to the previously discovered Langermannia gigantean (DQ112623) and L. gigantean (LN714562) from northern Europe, and Mycena (Pakistan) showed a 97% similarity to M. leaiana (MF686520) and M. leaiana (MW448623) from the USA. UV-vis, scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD) were used for AgNPs’ characterization. The UV-vis absorption peak of 500–600 nm indicates the AgNPs’ presence. XRD results determined Calvatia gigantea AgNPs were nanocrystals and Mycena leaiana seems to be amorphous. In addition, SEM results showed the cubic morphology of C. gigantea with a diameter of 65 nm, and the FTIR spectra of fruiting body revealed the presence of functional groups—carboxyl, nitro, and hydroxyl—in AgNPs, which catalyzed the reduction of Ag+ to Ag0. Further antibacterial activity of mushrooms against MDR strains was determined via agar well diffusion assay, and Minimum Inhibitory Concentration (MIC) was estimated by qualitative experimentation using the broth dilution method. All experiments were conducted in triplicate. The results showed that the mushroom AgNPs, along with their synergy and nano-composites (with the exception of Ethyl-acetate), were shown to have zones of inhibition from 4 mm to 29 mm against multidrug-resistant pathogens such as Acinetobacter baumannii, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumonia, Proteus mirabilis, Enterobacter cloacae and Escherichia coli. The mushroom composites were active against most of the tested microorganisms whilst the lowest MIC value (10–40 mg/mL) was recorded against MDR strains. Hence, the present study suggested the possibility of employing compounds present in mushrooms for the development of new antibacterial agents, as well as efflux pump inhibitors.
Relevance of local compound‐specific transverse dispersion for conservative and reactive mixing in heterogeneous porous media

Different measures of dilution have been proposed to describe solute mixing in heterogeneous porous media. Most of these approaches lead to the definition of effective dispersion coefficients. In order to quantify mixing, these up‐scaled parameters should account for both local‐scale dispersion and effects of flow variability in heterogeneous formations (e.g., flow focusing in high‐conductivity and defocusing in low‐conductivity inclusions). The correct quantification of mixing is particularly important for transport of compounds undergoing reactions. Recent results of multitracer laboratory experiments showed a dependency of local transverse dispersion on molecular diffusion over a wide range of flow velocities, implying compound‐specific transverse mixing even at intermediate and high Péclet numbers. The goal of this study is to assess the relevance of a compound‐specific local‐scale transverse dispersion on conservative and reactive mixing in heterogeneous domains at the field scale. We restrict our analysis to steady state two‐dimensional flow and transport with continuous injection from a line source. We present numerical simulations in heterogeneous domains with different characteristics of variability in the conductivity field, and apply as measures of solute mixing: (1) the effective transverse dispersion coefficient derived from second central spatial moments, (2) a dispersion coefficient derived from flux‐related second central spatial moments, (3) the scalar dissipation rate, and (4) a dispersion coefficient derived from the flux‐related dilution index. The results indicate compound‐specific transverse mixing behavior also at the field scale which is particularly significant in case of low to moderately heterogeneous porous media. Moreover, we show that measures of dilution calculated in a flux‐related framework result in an improved quantification of mixing processes and allow to define up‐scaled parameters (i.e., effective transverse dispersion coefficients) affected by a low degree of uncertainty. For mixing‐controlled reactive transport we illustrate the importance of compound‐dependent local effects on the length of reactive solute plumes.
Pattern and Socio-demographic characteristics of Drug Users at the National Drug Law Enforcement Agency (NDLEA) Rehabilitation Facility, Port Harcourt

Background: Substance abuse particularly among young people has become a large phenomenon globally affecting all segments of society. The abuse of alcohol, tobacco, cannabis and other psychoactive drugs among young people has become an issue of public health concern with untold negative consequences on human existence. Aim: This study sought to examine the sociodemographic profiles and patterns of drug use among drug users at the NDLEA Rehabilitation Facility, Port Harcourt. Materials and Methods: This was a descriptive cross-sectional study conducted among inmates of the National Drug Law Enforcement Agency (NDLEA), Port Harcourt. A structured questionnaire covering socio-demographic characteristics and other factors were self-administered to inmates of the facility, who have been brought by their relative for addiction care over a period of 3 years (2017 to 2020). Ethical approval was obtained from the ethical committee of the University of Port Harcourt Teaching Hospital and approval was obtained from the NDLEA Authority. All other ethical provisions were followed. Descriptive statistics was used to analyzed the data. Data were analyzed with number count, percentage, and then Chi-square of independence. Results: Majority of the drug users were male (98,8%), single (72.5%), unemployed (27.5%) and apprentice (40.0%), between the ages of 15 and 35 (67.5%) and with tertiary education. Cannabis was the most consumed drug (75.7%), followed by nicotine (30.8%) alcohol (28.3%), cocaine (27.4%) and heroine (25.8%). Majority of the users were introduced to drug by friends and family members and referred to the feeling they got on the first day of use as high and happy. Majority had 15 to 25 years as age of onset of drug use and there were no family history of psychoactive substance use or mental illness. Conclusion: Substance use is common among young people between the ages of 26 and 30, single, with higher level of education and low-income earners. Majority use illicit drugs, which they started at early age of 15 to 25 and introduced to by friends and family members. Improvement in socio-economic status of adolescents and sustained public health enlightenment will help to reduce the rising prevalence of drug use.
Econophysics: Quantitative Studies of Equity and Credit Markets

How can we understand the inherent risks of our economy and, in particular, of the financial sector? How stable is our economy? How resilient to crisis? These questions have garnered a lot of attention since the beginning of the recent financial crisis. Econophysics can provide valuable contributions. It has established itself as an interdisciplinary field of research, striving to understand the economy as a complex system in its own right. Here we consider two areas of econophysics: empirical studies of equity markets and credit risk modeling. Regarding equity markets we focus on statistical dependencies and non-stationarity. How can we measure correlations between time series reliably, although statistical features of the single time series, as well as their dependence are constantly changing? How do correlations change on different time scales? And how strong are nonlinear effects? We have to address these important questions before we can turn our attention to the time dependence of correlations. A detailed study of the changes in the correlation structure finally reveals clearly distinguishable market states. We observe that the market frequently jumps back and forth between different market states. On longer time scales we find an overall evolution towards new states. The abundance of data on equity markets allows for a direct empirical approach in this area. For credit risk, however, empirical data are scarce and difficult to obtain. Therefore we first choose a model-based approach to develop an intuition and understanding of credit risk. We consider the Merton model, a structural model for zero coupon bonds, where the total asset value of an obligor is described by a stochastic process. Credit defaults and losses are directly determined by the asset value at maturity. This simple model already allows to pinpoint the key differences between equity and credit portfolios. For equity investments, the risk of large losses is roughly balanced by the chance of equally large gains. The same does not hold for credit contracts, where the losses may have a small probability to occur, but their magnitude can by far exceed the largest possible gain. Due to this asymmetry the risk of large portfolio losses cannot be reduced by increasing the number of contracts in the portfolio. The benefit of diversification is severely limited, as soon as even weak correlations between the obligors' asset values are taken into account. Even though the Merton model makes many simplifying assumptions, it can provide more than just qualitative insights into credit risk. Indeed we demonstrate that empirical credit data are well-described by our analytical results for the Merton model.
Robust Practical Stabilization of Nonlinear Systems With Saturated Impulsive Control

What we focus on in this brief is the robust practical stabilization (RPS) problem for the impulsive system involving external disturbance, where the impact of actuator saturation on impulses is fully considered. Based on convergent strength of continuous dynamics of the system in the sense of actuator saturation, some sufficient conditions for RPS are presented by designing saturated impulsive controllers. In addition, the control gain is obtained by solving the problem in the form of linear matrix inequalities. Finally, an example about the Chua’s oscillator demonstrates the effectiveness of the obtained result.
Effect of Mindfulness-based Interventions on Mental Health of Women with Infertility: A Narrative Review

Background: By instinct, human beings have desire to propagate their genes. Infertility can be very painful for the individuals. The men and women with this medical condition are not just battling physiological problems but also dealing with psychological, emotional, and social battles, including low self-esteem, stress, depression, frustration, hopelessness, anxiety, feeling of guilt and worthlessness, insecurity in marital relationship, marital discords and lesser marital satisfaction. Women population is more vulnerable to the psycho-social consequences of infertility. Though many research studies have been conducted to investigate the psycho-social impact of infertility on women, the research literature on the combative role of mindfulness-based interventions on mental health of women have been limited. Mindfulness as a psycho-therapeutic intervention has been shown to be effective in chronic conditions like cancer, diabetes, anxiety, depression and pain. The mindfulness-based interventions in individuals with chronic conditions can assist them to accept the condition and overcome the psychological issues that arise due to the physical health conditions. Infertility is a physical health condition that has strong psychological consequences. Thus, there is a need to study the impact of these interventions on women population suffering from infertility. The purpose of the present study is to explore the effect of mindfulness-based interventions on the mental health of the women with infertility. Objective: In light of the foregoing history, the current review's research question is “Are mindfulness-based interventions effective in improving mental health of women with infertility? ” Methods: This is a narrative review guided by systematic approach to searching. Prominent research databases were used to locate empirical articles reporting on the efficacy of mindfulness-based therapies on mental health of infertile women between 2000 and 2020. There were no restrictions on participant demographics including age, sex, geography, socioeconomic status, or year of publication. Only empirical studies which investigated mindfulness-based interventions on mental health (anxiety, stress, depression, quality of life and psychological well-being) of infertile women were included in the review. Results: Seventeen papers were considered in the review which involved 983 females. Depression, anxiety, stress, quality of life and psychological well-being were taken as measures of mental health of infertile women. The studies have confirmed that the mindfulness-based interventions are highly helpful for women with infertility. The interventions have successfully reduced stress, anxiety and depressive symptoms among the participants as well as enhanced their quality of life and psychological well-being.
Association of gut microbiota composition and craniosynostosis

Background Gut microbiota has been reported to be associated with a series of metabolic diseases including metabolic bone disease. However, study about gut microbiota and craniosynostosis (CS) is very rare. We aim to investigate the gut microbiota composition in CS patients and assess the possible relationship. Methods A total of 30 infants with CS and 30 infants with non-CS treated in Children’s Hospital of Nanjing Medical University of Jiangsu Province from June 2021 to March 2022 were finally included in this study. All processing and analysis are carried out using 16S ribosomal RNA (rRNA) high-throughput gene sequencing. Results The CS group have significantly lower levels of family, genus, and species than non-CS group (all P<0.05). Furthermore, Staphylococcales and Lactobacillales at the order level, Enterococcaceae and Staphylococcaceae at the family level, and Enterococcus and Staphylococcus at the genus level were significantly enriched in the CS group (all P<0.05). Additionally, functional prediction showed that six metabolic pathways significantly differed between the two groups (all P<0.05). Of those, pathways involving polycyclic aromatic hydrocarbon degradation (P=0.030) and penicillin and cephalosporin biosynthesis (P=0.027) were more abundant in CS group than in non-CS group. Conclusions Gut microbiota was statistically associated with the development of CS, and several taxa and specific functional pathways with significantly altered abundance have been identified in CS patients. These findings can provide clues for the study on the mechanism and early diagnosis of CS.
Effect of Irrigation Water Level and N-fertilizer Rate on Yield and Water Productivity of Wheat Under Furrow Irrigation at Tibila Irrigation Scheme, Arsi Ethiopia

The response of wheat yield to different levels of irrigation and varying amounts of nitrogen fertilizer was investigated from 2020-2022 GC at Tibila irrigation scheme. Three levels of irrigation (70, 85, and 100% ETc) and three nitrogen rates (46, 69, and 92 kg/ha) were arranged in two factorial combination in Randomized Complete Block Design with three replications. Recently released bread wheat variety king-bird was used as test crop. The experimental field was divided into 27 plots with plot size of 4m x 6m dimension to accommodate five furrows with spacing of 60cm and having 6m length. From the result, it is found that, irrigation and nitrogen levels both had a considerable impact on wheat grain yield. The analysis of variance result revealed that the maximum grain yield (5.88 tha -1 ) of wheat was recorded at 92 kg/ha nitrogen rate and 100% ETc irrigation level. The minimum grain yield (3.98 tha -1 ) was obtained from 46 kg/ha nitrogen and 70% ETc irrigation treatment. Similarly, the study revealed that other yield components like plant height, spike length, number of seed per spike, productive tiller number and above ground biomass of wheat increased with the increasing rates of nitrogen fertilizer and irrigation water level. Here, increasing the application rate of nitrogen fertilizer from (46-92) kgh -1 and water level from 70% ETc to full irrigation maximize yields of wheat. On the other hand, reducing water level from 100 to 85% ETc and N-fertilizer rate from 92 to 69 kg/ha was not reduce the yield significantly, rather it have water saving and economic advantage. Moreover the partial budget analysis revealed that an application of 85% ETc and 69 kg/ha nitrogen fertilizer is the best treatment to obtain an optimum yield and maximum benefit cost ratio in the study area. Therefore, application of 85% ETc irrigation and 69 kg/ha nitrogen is recommended for optimum returns of irrigation and nitrogen fertilization of wheat in the area.
Determinants of Cost Inefficiency and Farmer Performance in Broiler Contract Farming

The broiler industry plays an important role in meeting the growing demand for animal protein. Ensuring favorable farming conditions are needed to maintain the meat supply, and theoretically, this can be improved through the implementation of Contract Farming (CF). CF grants farmers the privilege to predict quantities, prices, and reduce production risks. However, one of the key challenges in establishing CF is the cost efficiency and performance of farmers. This study aims to develop a cost function for farmers, identify factors contributing to inefficiency, and evaluate farmer performance. The purposive sampling method is employed to select broiler farmers participating in contract farming as the sample for this study. Primary data were collected through surveys. Stochastic frontier cost analysis is utilized to derive a broiler cost function while examining the causes of farm inefficiency and their relationship with farmers’ performance variables. The results indicate that the broiler cost function is significantly influenced by labor costs, the price of day-old chickens, feed expenses, and harvest tonnage. Meanwhile, the inefficiency effect is substantially influenced by farmer age, education, household size, experience, and mortality ratio (MR). Reducing the MR can increase broiler yield, directly improving cost efficiency and, thus farmers’ income. Nonetheless, a comprehensive approach that includes training, monitoring, feedback, and incentivization is needed to enhance farmer performance in broiler contract farming.
Studies of solute transport through fractured till in Iowa

viii GENERAL INTRODUCTION 1 Purpose and Scope 2 Dissertation Organization 4 FRACTURE-DOMINATED TRANSPORT OF NITRATE AND ATRAZINE THROUGH TILL IN IOWA 5 Abstract 5 Introduction 6 Materials and Methods 8 Results and Discussion 17 Conclusions 23 Acknowledgements 25 References 25 COMPARISON OF FORWARD MODELING APPROACHES TO SIMULATE SOLUTE TRANSPORT THROUGH FRACTURED TILL 39 Abstract 39 Introduction 40 Methods 48 Models 51 Results 56 Conclusions 63 Acknowledgements 65 References 65 SIMULATION OF SOLUTE TRANSPORT THROUGH FRACTURED TILL USING A STOCHASTIC, 3-DIMENSIONAL, DISCRETE FRACTURE MODEL 81 Abstract 8