Miracle-dz/UniFAR-FTUs huggingface dataset:
A comprehensive description of the TolC effect on the antimicrobial susceptibility profile in Enterobacter bugandensis

Background Enterobacter bugandensis is an emerging human pathogen in which multidrug resistant strains have been continuously isolated from various environments. Thus, this organism possesses the potential to pose challenges in human healthcare. However, the mechanisms, especially the efflux pumps, responsible for the multidrug resistance in E. bugandensis remain to be well elucidated. Methods The Enterobacter strain CMCC(B) 45301 was specifically identified using whole genome sequencing. The specific CMCC(B) 45301 homologues of the TolC dependent efflux-pump genes characterized in Escherichia coli were identified. The tolC deletion mutant in CMCC(B) 45301 was constructed and subjected to susceptibility tests using 26 different antimicrobial agents, along with the wild type strain. The synergistic effects combining the Bacillus crude extract (BCE) and several other TolC-affected compounds against CMCC(B) 45301 were assayed. Results We reclassified the Enterobacter CMCC(B) 45301 strain from species cloacae to bugandensis, on the basis of its whole genome sequence. We found that the CMCC(B) 45301 TolC, AcrAB, AcrD, AcrEF, MdtABC, EmrAB, and MacAB exhibit high similarity with their respective homologues in E. coli and Enterobacter cloacae. Our results for the susceptibility tests revealed that lacking tolC causes 4- to 256-fold decrease in the minimal inhibitory concentrations of piperacillin, gentamicin, kanamycin, tetracycline, norfloxacin, ciprofloxacin, chloramphenicol, and erythromycin against CMCC(B) 45301. In addition, the inhibition zones formed by cefuroxime, cefoperazone, amikacin, streptomycin, minocycline, doxycycline, levofloxacin, florfenicol, trimethoprim-sulfamethoxazole, azithromycin, lincomycin, and clindamycin for the tolC mutant were larger or more obvious than that for the parent. Our data suggested the important role played by TolC in CMCC(B) 45301 susceptibility to common antibiotic families covering ß-lactam, aminoglycoside, tetracycline, fluoroquinolone, phenicol, folate pathway antagonist, macrolide, and lincosamide. Deletion for tolC also increased the susceptibility of CMCC(B) 45301 to berberine hydrochloride and BCE, two natural product-based agents. Finally, we found that erythromycin, norfloxacin, and ciprofloxacin can potentiate the antibacterial activity of BCE against CMCC(B) 45301. Discussion The present study elaborated the comprehensive TolC effect on the antimicrobial susceptibility profile in E. bugandensis, which might contribute to the development of more therapeutic options against this nosocomial pathogen.
Isolation of living dopaminergic neurons labeled with a fluorescent ligand of the dopamine transporter from mouse substantia nigra as a new tool for basic and applied research

Dopaminergic neurons (DNs) of the nigrostriatal system control the motor function, and their degeneration leads to the development of Parkinson’s disease (PD). A stumbling block in the study of DNs in the whole substantia nigra (SN) is the lack of tools to analyze the expression of most of the genes involved in neurotransmission, neurodegeneration, and neuroplasticity, since they are also expressed in other cells of the SN. Therefore, this study aimed to develop a fluorescence-activated cell sorting method for isolating living DNs from the SN of wild-type mice using two fluorescent dyes, DRAQ5 (nuclear stain) and a dopamine uptake inhibitor GBR 12909 coupled to a fluorophore (DN stain). We have developed a method for selecting a population of DNs from the SN of mice, as evidenced by: (i) immunopositivity of 95% of the sorted cells for tyrosine hydroxylase, the first enzyme of dopamine synthesis; (ii) the sorted cells expressing the genes for specific proteins of the dopaminergic phenotype, tyrosine hydroxylase, the dopamine transporter, and vesicular monoamine transporter 2 and non-specific proteins, such as aromatic L-amino acid decarboxylase, non-specific enzyme of dopamine synthesis. We then compared the changes in gene expression found in the sorted DNs and in the SN homogenate in a PD model we developed, reproduced in mice by treatment with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Using quantitative PCR, we obtained evidence of the same changes in the expression of specific genes in the sorted DNs of SN and in the SN homogenate of a MPTP mouse model of PD, compared with the control. The undoubted advantage of our approach is the possibility of obtaining a large amount of readily available and relatively cheap primary material (SN) from wild-type mice, which can be used to solve both research and applied problems. In addition, this method can be easily adapted to the isolation of DNs from the SN in other animal species, including non-human primates.
A window into magnetic reconnection: IRIS observations of the consequences of reconnection during solar flares

Magnetic reconnection is a dynamic process that occurs in solar flares in a tenuous and hot environment. High-cadence, high-spatial resolution spectroscopic observations with the Interface Region Imaging Spectrometer (IRIS) have provided a unique window into the reconnection process that occurs during solar flares. IRIS has observed many consequences of the reconnection process, including detailed observations of outflows that are thought to be indicative of reconnection, possible observations of the termination shocks that are predicted by-products of reconnection, and observations of flare ribbons which are imprints of the reconnection process in the chromosphere. This paper will review these observations and put them in the context of flare models that predict reconnection signatures.
Numerical Simulations of a Gravity Wave Event over CCOPE. Part I: The Role of Geostrophic Adjustment in Mesoscale Jetlet Formation

Abstract Mesoscale model simulations are performed in order to provide insight into the complex role of jet streak adjustments in establishing an environment favorable to the generation of gravity waves on 11–12 July 1981. This wave event was observed in unprecedented detail downstream of the Rocky Mountains in Montana during the Cooperative Convective Precipitation Experiment. The high-resolution model simulations employ a variety of terrain treatments in the absence of the complicating effects of precipitation physics in order to examine the complex interactions between orography and adiabatic geostrophic adjustment processes. Results indicate that prior to gravity wave formation, a four-stage geostrophic adjustment process modified the structure of the mid- to upper-tropospheric jet streak by creating secondary mesoscale jet streaks (jetlets) to the southeast of the polar jet streak in proximity to the gravity wave generation region (WGR). During stage I, a strong rightward-directed ageostrophic flow i.
Post-COVID-19 human memory impairment: A PRISMA-based systematic review of evidence from brain imaging studies

Many people with coronavirus disease 2019 (COVID-19) report varying degrees of memory impairment. Neuroimaging techniques such as MRI and PET have been utilized to shed light on how COVID-19 affects brain function in humans, including memory dysfunction. In this PRISMA-based systematic review, we compared and summarized the current literature looking at the relationship between COVID-19-induced neuropathological changes by neuroimaging scans and memory symptoms experienced by patients who recovered from COVID-19. Overall, this review suggests a correlational trend between structural abnormalities (e.g., cortical atrophy and white matter hyperintensities) or functional abnormalities (e.g., hypometabolism) in a wide range of brain regions (particularly in the frontal, parietal and temporal regions) and memory impairments in COVID-19 survivors, although a causal relationship between them remains elusive in the absence of sufficient caution. Further longitudinal investigations, particularly controlled studies combined with correlational analyses, are needed to provide additional evidence.
Humoral immune response following a third SARS-CoV-2 mRNA vaccine dose in solid organ transplant recipients compared with matched controls

Background Solid organ transplant (SOT) recipients have shown suboptimal antibody response following COVID-19 vaccination. Several risk factors for the diminished response have been identified including immunosuppression and older age, but the influence of different comorbidities is not fully elucidated. Method This case-control study consisted of 420 Danish adult SOT recipients and 840 sex- and age-matched controls, all vaccinated with a third homologous dose of either BNT162b2 (Pfizer–BioNTech) or mRNA-1273 (Moderna) vaccine. The primary outcome was differences in humoral immune response. The secondary outcome was breakthrough infections. Additionally, we looked for factors that could predict possible differences between the two groups. Results Response rate increased from 186/382 (49%) to 275/358 (77%) in SOT recipients and remained on 781/790 (99%) to 601/609 (99%) in controls following a third vaccine dose. SOT recipients had significantly lower median antibody concentrations after third dose compared to controls (332.6 BAU/ml vs 46,470.0 BAU/ml, p <0.001). Lowest median antibody concentrations were seen in SOT recipients with liver disease (10.3 BAU/ml, IQR 7.1-319) and diabetes (275.3 BAU/ml, IQR 7.3-957.4). Breakthrough infections occurred similarly frequent, 150 (40%) among cases and 301 (39%) among controls (p = 0.80). Conclusion A third COVID-19 vaccine dose resulted in a significant increase in humoral immunogenicity in SOT recipients and maintained high response rate in controls. Furthermore, SOT recipients were less likely to produce antibodies with overall lower antibody concentrations and humoral immunity was highly influenced by the presence of liver disease and diabetes. The prevalence of breakthrough infections was similar in the two groups.
Home-based portable fNIRS-derived cortical laterality correlates with impairment and function in chronic stroke

Introduction Improved understanding of the relationship between post-stroke rehabilitation interventions and functional motor outcomes could result in improvements in the efficacy of post-stroke physical rehabilitation. The laterality of motor cortex activity (M1-LAT) during paretic upper-extremity movement has been documented as a useful biomarker of post-stroke motor recovery. However, the expensive, labor intensive, and laboratory-based equipment required to take measurements of M1-LAT limit its potential clinical utility in improving post-stroke physical rehabilitation. The present study tested the ability of a mobile functional near-infrared spectroscopy (fNIRS) system (designed to enable independent measurement by stroke survivors) to measure cerebral hemodynamics at the motor cortex in the homes of chronic stroke survivors. Methods Eleven chronic stroke survivors, ranging widely in their level of upper-extremity motor deficit, used their stroke-affected upper-extremity to perform a simple unilateral movement protocol in their homes while a wireless prototype fNIRS headband took measurements at the motor cortex. Measures of participants' upper-extremity impairment and function were taken. Results Participants demonstrated either a typically lateralized response, with an increase in contralateral relative oxyhemoglobin (ΔHbO), or response showing a bilateral pattern of increase in ΔHbO during the motor task. During the simple unilateral task, M1-LAT correlated significantly with measures of both upper-extremity impairment and function, indicating that participants with more severe motor deficits had more a more atypical (i.e., bilateral) pattern of lateralization. Discussion These results indicate it is feasible to gain M1-LAT measures from stroke survivors in their homes using fNIRS. These findings represent a preliminary step toward the goals of using ergonomic functional neuroimaging to improve post-stroke rehabilitative care, via the capture of neural biomarkers of post-stroke motor recovery, and/or via use as part of an accessible rehabilitation brain-computer-interface.
Optimal control of time-delay systems by dynamic programming

The use of iterative dynamic programming employing systematic region contraction and accessible grid points is investigated for the optimal control of time-delay systems. At the time of generating the grid points for the state variables, the corresponding delayed variables at each time stage are also generated and stored in memory. Then, when applying dynamic programming, a linear approximation is used to obtain the initial profile for the delayed variables during integration. This procedure was tested with four problems of different complexity. In each case the optimal control policy is easily obtained and the results compare very favourably with those reported in the literature using other computational procedures.
Teacher Practices Aimed at Preventing School Bullying: A Comparative Analysis of Lithuania and Norway

This study investigates similarities and differences in Lithuanian and Norwegian teacher practices aimed at preventing school bullying by applying a whole-school approach anti-bullying programme. The quantitative data was collected from 1576 teachers from 99 schools in Lithuania, and 82 teachers from 13 schools in Norway that have implemented the Olweus Bullying Prevention Programme (OBPP). The comparative analysis of the study results indicates that Norwegian teachers are slightly more active in working with the OBPP on the school and individual levels, as well as in working with the programme in general. The study reveals that female teachers are more active than male teachers on the classroom and individual levels of the OBPP as well as the whole programme, and that primary education teachers are more active than lower secondary education teachers on the classroom level of the OBPP. The implications of teacher practices aimed at preventing bullying by applying the OBPP are discussed, and limitations of the current study emphasised.
HOAPS: A new satellite-derived freshwater flux climatology

HOAPS (Hamburg Ocean Atmosphere Parameters and Fluxes from Satellite Data) is a global climatology of sea surface parameters and surface energy and freshwater fluxes derived from satellite radiances for the time period July 1987 to December 1998. Data from polar orbiting radiometers, the Special Sensor Microwave/Imager (SSM/I) and the Advanced Very High Resolution Radiometer (AVHRR), have been used to get global fields of surface meteorological and oceanographic parameters but also latent heat flux, evaporation, precipitation and net freshwater flux over ice free ocean areas for various averaging periods and grid sizes. All retrieval methods have been validated with in situ data on a global scale to the extent possible. In this paper some of the major outcomes are exemplarily shown together with the results of comparison studies with the in situ climatology provided by the Southampton Oceanography Centre (SOC).
Fully Modified Estimation in Cointegrating Polynomial Regressions: Extensions and Monte Carlo Comparison

We study a set of fully modified (FM) estimators in multivariate cointegrating polynomial regressions. Such regressions allow for deterministic trends, stochastic trends, and integer powers of stochastic trends to enter the cointegrating relations. A new feasible generalized least squares estimator is proposed. Our estimator incorporates: (1) the inverse autocovariance matrix of multidimensional errors and (2) second-order bias corrections. The resulting estimator has the intuitive interpretation of applying a weighted least squares objective function to filtered data series. Moreover, the required second-order bias corrections are convenient byproducts of our approach and lead to a conventional asymptotic inference. Based on different FM estimators, multiple multivariate KPSS-type of tests for the null of cointegration are constructed. We then undertake a comprehensive Monte Carlo study to compare the performance of the FM estimators and the related tests. We find good performance of the proposed estimator and the implied test statistics for linear hypotheses and cointegration. JEL Classification: C12, C13, C32
Quality of Life in Sudanese Women with Breast Cancer in Khartoum Oncology Hospital, 2017

Background: Breast cancer is the most common cancer among women in Sudan and over the world. The concerning mainly was on clinical management but health-related quality of life now is thought to be an important endpoint in clinical trials. Assessing the quality of life in cancer patients contribute to increase the value of treatment and could play a role as prognostic factor within medical parameters. This research presents the outcome of quality of life in Sudanese women with breast cancer depending on international and regional result. Objective: The purpose of this study was to assess the quality of life of Sudanese women with breast cancer who came to Khartoum Oncology Hospital. Methods: The study was a hospital based cross-sectional research conducted on 114 breast cancer patients from November 2017 to December 2017. Standardized questionnaire of European organization for research and treatment of cancer QoL questionnaires QLQ-C30 (Quality of Life Questionnaire-Cancer 30) and QLQ-BR23 (Quality of Life Questionnaire-Breast Cancer 23) was used after little modification according to the researcher’s participant’s acceptance. The data collection was piloted to assess the questionnaire acceptance, clarity and completion time and no modification were made. The data and analysis were made by using SPSS version 19, most of the scales have excellent internal consistency except for social functioning item has low internal consistency, Analysis of Variance (ANOVAs) was performed to examine the relationship between independent variables and functional and symptom scales of both questionnaires. Results: The participants mean age was (Mean=48.2 SD=12.199) years (Mean ± SD). Sudanese patients with breast cancer have high Functional score and lower symptom score in both EORTC QLQ-C30 and the EORTC BR- 23 scores. For Functional scale Most Scores are high above 80%, ranging from (Mean=83.7 SD=23.6) which for Social functioning to the least score was for Physical functioning (Mean=67 SD=29). Emotional functioning (Mean=73.97 SD=31). The Global health scale has moderate score (Mean=67 SD=18.85). Within the Symptom scales / items all scales scored below 30 which mean they have no more symptoms except for financial difficulty item scored 45%. Most of the socio-demographic variables, except the Age of participants, did not show significant association with QoL of the participants. Concerning the modality of treatment Surgery had association with QoL. Conclusion: The quality of life among Sudanese women with breast cancer is good in compared to many countries. But measures should be taken to improve their financial support.
Aspect Ratio Effect on Natural Convection Flow in a Cavity Submitted to a Periodical Temperature Boundary

The effect of aspect ratio on natural convection flow in a cavity submitted to periodic temperature boundary, is investigated numerically. The temperature of the heated wall is either maintained constant or varied sinusoidally with time while the temperature of the opposite vertical wall is maintained constant. The results are given for a range of varied parameters as Rayleigh number (5 X 10 3 ≤ Ra≤10 6 ), cavity aspect ratio (1/6≤ A ≤8), and period of the sinusoidally heated wall (1 ≤ π ≤1600). The amplitude of oscillation (a=0.8) and the Prandtl number (Pr=0.71) were kept constant. The results obtained in the steady state regime show that the heat transfer averaged over the cold wall is maximum when the aspect ratio is in the range 1 ≤A≤ 2. In the case of a periodic temperature boundary, it is shown that the deviation between the mean heat transfer and the heat transfer of the constant heated case is larger for shallow cavities.
Collaborating around Digital Tabletops

We present a study of children collaborating around interactive tabletops in three different countries: India, the United Kingdom and Finland. Our data highlights the key distinctive physical strategies used by children when performing collaborative tasks during this study. Children in India employ dynamic positioning with frequent physical contact and simultaneous object movement. Children in the UK tend to prefer static positioning with minimal physical contact and simultaneous object movement. Children in Finland use a mixture of dynamic and static positioning with minimal physical contact and object movement. Our findings indicate the importance of understanding collaboration strategies and behaviours when designing and deploying interactive tabletops in heterogeneous educational environments. We conclude with a discussion on how designers of tabletops for schools can provide opportunities for children in different countries to define and shape their own collaboration strategies for small group learning that take into account their different classroom practices.
Analytical treatment of source terms for complex channel geometry

Starting from the classical conservative form of the shallow water equations, the source term of the momentum balance equation was modified to increase computational stability. This was achieved by replacing the term representing the local bed slope by an alternative expression of the pressure effect due to cross-section irregularities in non-prismatic channels. The resulting mathematical model turns out to be particularly suitable for complex channel and natural river geometries, and also improves the computational stability for complicated flow conditions. The explicit finite difference MacCormack scheme was adopted for numerical implementation. The model was thoroughly tested using a set of numerical test cases involving various channel geometries and a wide range of flow conditions. The same simulations were compared also with the classical model and with other schemes. Finally, a real flood event on the Italian river Reno was simulated, to confirm the model suitability for natural channels.
Working Paper 217 African Continental Free Trade Agreement: A Review of Analyses of Likely Impacts and Challenges of Implementation

role with over 70 percent, resulting in a significant transformative impact if successfully implemented. Fina lly, various factors, such as public awareness of the agreement, challenges related to a person’s free mobility and capital, reconciliation of domestic policies, and related adjustment costs and inequality impacts can affect the effects predicted by current models compared to the actual effects of the outcomes of the AfCFTA over time.