Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantifying the contribution of four resistance mechanisms to ciprofloxacin minimum inhibitory concentration in Escherichia coli: a systematic review

Introduction Ciprofloxacin resistance in Escherichia coli is widespread and adds to the burden of E. coli infections. Reviews assessing the genetic basis of ciprofloxacin resistance have mostly been qualitative. However, to allow for the prediction of a resistance phenotype of clinical relevance based on genotypic characteristics, it is essential to quantify the contribution of prevalent genotypic determinants to resistance. We carried out a systematic review to assess the relative contribution of currently known genomic resistance determinants to the minimum inhibitory concentration (MIC) of ciprofloxacin in E. coli. Methods PubMed and Web of Science were searched for English language studies that assessed both ciprofloxacin MIC and the presence or introduction of genetic determinants of ciprofloxacin resistance in E. coli. We included experimental and observational studies without time restrictions. Medians and ranges of MIC fold changes were calculated for each resistance determinant and for combinations of determinants. Results We included 66 studies, describing 604 E. coli isolates that carried at least one genetic resistance determinant. Genes coding for targets of ciprofloxacin (gyrA and parC) are strongest contributors to ciprofloxacin resistance, with median MIC fold increases ranging from 24 (range 4-133) for single Ser83Leu (gyrA) mutants to 1533 (range 256-8533) for triple Ser83Leu, Asp87Asn/Gly (gyrA) and Ser80Ile/Arg (parC) mutants. Other resistance mechanisms, including efflux, physical blocking or enzymatic modification, conferred smaller increases in ciprofloxacin MIC (median MIC fold increases typically around 15, range 1-125). However, the (combined) presence of these other resistance mechanisms further increases resistance with median MIC fold increases of up to 4000, and even in the absence of gyrA and parC mutations up to 250. Conclusion This report provides a comprehensive and quantitative overview of the contribution of different genomic determinants to ciprofloxacin resistance in E. coli. Additionally, the data demonstrate the complexity of resistance phenotype prediction from genomic data and could serve as a reference point for studies aiming to address ciprofloxacin resistance prediction using genomics, in E. coli.
Risk-adjusted and Bonferroni-adjusted seasonality in emerging Asian stock markets

Existing literature on market seasonality focuses mainly on returns anomalies with little or no attention to risk adjustment. This study investigates risk-adjusted, and Bonferroni adjusted day-of-the-week anomalies in nine emerging Asian stock markets. The data consist of the daily prices of nine stock indices from January 1997 to September 2019. The MSCI emerging market index was employed as a proxy of time-varying risk. Findings/originality : The results confirm the presence of day-of-the-week anomalies in emerging Asian markets, and the addition of the market risk proxy has failed to fade these patterns. Finally, after consideration of time-varying risk premium and applying Bonferroni Correction type adjustment, several market anomalies remain. However, both adjustments partially eliminate the significance of these patterns. The presence of these anomalies suggests that little of this can be accounted for the MSCI-EM stock price index. The results also confirm that systematic risk level varies from Monday to Friday.
Methicillin-resistant Staphylococcus aureus update: resistance genes and their influence on the detection of methicillin-resistant Staphylococcus aureus for screening purposes

Methicillin-resistant Staphylococcus aureus (MRSA) is a serious problem in healthcare settings leading to increased costs, length of stays, morbidity, and mortality. This article reviews certain findings on the global transmission of MRSA during the last decade and gives an overview of several different diagnostic tests on the market used to identify colonized patients.
Health Risk Assessment of Heavy Metals in Clarias gariepinus (Burchell, 1822) from Fish Mongers within Akure Metropolis, Ondo State, Nigeria

 Abstract — The concentration of heavy metal (Cd, Pb, Fe, Zn, Cu) in Clarias gariepinus collected from fish markets; Fanibi (Station I) and Fiwasaye (Station II) in Akure metropolis, Ondo state, Nigeria were investigated to ascertain the safety for the consumers. 60 samples were collected from the two markets in three batches (I, II, III) for a period of six months and analyzed for heavy metals in the gills and muscles of the fish. Also, the Health Risk Index (HRI) was used to determine the health risk of these metals to the consumer. The results showed that the investigated metal concentration was higher in station I than station II, except Pb having higher concentration in station II than station I. In both stations, the highest concentration of Fe was recorded in the gills (12.60 ± 1.51; 6.94 ± 1.38) and muscles (3.72 ± 0.09; 3.86 ± 0.33) of samples in batch I. Also, the HRI revealed that consumption of Clarias gariepinus from these study areas did not pose any health risk (HRI < 1). In addition, concentrations of the heavy metals were all below the permissible limits recommended by FAO/WHO.
Estimation and comparison of reference evapotranspiration within Kaduna Central District, Nigeria, using four different methods

The reference evapotranspiration (ETo) within Kaduna Central District, Nigeria was estimated from a 30-year climatological data using four different methods namely, Penman-Monteith (PM), Blaney Criddle (BC), Hargreaves (HGRV) and Piche evaporimeter (PiEv) (atmometer) methods. The study shows that the highest ETo values obtained from PM, BC and PiEv were 6.43 mm/day, 7.58 mm/day and 8.63 mm/day, respectively, and these occurred in February, except for HGRV which estimated its highest ETo (3.73 mm/day) in March. The lowest ETo values were obtained in August for all the methods. By means of the confidence index (c), agreement or concordance index (d) and correlation coefficients (r) statistics the BC, HGRV and PiEv ETo values were correlated with that of PM, as the standard. Results showed that BC, HGRV and PiEv gave c-values of 0.88, 0.48 and 0.67, respectively. Hence, BC-PM, HGRV-PM and PiEv-PM correlations were adjudged as excellent, bad and good, respectively, on the basis of criteria for interpretation of the performance of methods of ETo estimations. Blaney-Criddle reference evapotranspiration method gave the best estimate in comparison to the Penman-Monteith standard in the study area. Hence, the Blaney-Criddle ETo can be calibrated with the Penman-Monteith ETo and used effectively within the Kaduna Central District conditions for irrigation water management decisions. Keywords: Estimation and comparison, Reference evapotranspiration, Methods, Kaduna Central District, Nigeria.
The profile of students conceptual understanding and procedural knowledge in solving geometry problems based on van hiele levels

This study aimed to describe the conceptual understanding and procedural knowledge of students in problem solving polyhedral in terms of the level of visualization, analysis and informal deduction and to investigate the correlation between conceptual understanding and procedural knowledge to problem solving. The method used was a mixed method that combines quantitative and qualitative methods. 297 Junior High School students from five different schools in Jember were selected as samples and three students were selected as the subject. That Determine the subject chosen by the van hiele test. The data were collected through tests and interviews. The results of the test van hiele obtained visualization level students as much as 44.5%, students’ level of analysis as much as 34.2%, informal deduction level students as much as 15.5% and 5.8% were classified at the level of pre-visualization. The results of the geometry test show that students at the visualization level meet some indicators of conceptual understanding but none of them meet the indicators of procedural knowledge, students at the level of analysis meet some indicators of conceptual understanding and procedural knowledge, while students with a level of deduction meet all indicators of conceptual understanding and procedural knowledge. The Results of the test showed that the higher the level of geometrical thinking students, the better the conceptual understanding and procedural knowledge.The results also showed that there was a significant relationship between conceptual understanding and procedural knowledge to solving the problem of 82.3% shown by the person correlation coefficient is 0.515 with a confidence level of 95% and a significant level α = 0.05. The better the conceptual understanding and procedural knowledge the better the ability to solve the problem.
Does camel milk have a positive impact on rat reproductive functions

Camel milk considered one of the most valuable food sources for nomadic people and has been consumed for centuries due to its nutritional values and medicinal properties. Camel milk has unique composition that differs from other ruminants' milk. It contains high minerals; vitamins and insulin contents but have low protein; cholesterol and sugar. This may give it its medicinal properties. Two experiments were done toinvestigate1-if camel milk has a positive impact on some aspects of reproductive functions and fertility in adult male rats, and 2- its effect on puberty in one month old male and female rats. In the first experiment twenty adult 6 months old male rats were used and were allocated into 2 equal groups (10 rats each). The control adult male rats were received (1 ml saline / kg BW) and treated adult male rats were received camel milk (1ml /kg BW) for 2 months by gastric gavage. Males from both groups were allowed to undergo monogamous pair mating. In the second experiment we studied the effect of camel milk on the puberty of one month old male and female rats. Control group [n=10(5male+5female)] were received (1ml /rat) and treated group [n=10 (5male+5female] were received camel milk (1ml saline /rat) for 1 month by gastric gavage. Results showed that camel milk administration caused a significant (p≤0.05) increase in antioxidant markers (GSH and SOD), sperm motility%, alive sperm%, sperm concentration, serum estrogen, progesterone levels, serum and testicular testosterone level and improves the conception rate, while, it caused a significant (p≤0.05) decrease of the sperm abnormalities%. Histologically, camel milk treated mature rats showed a significant (p≤0.05) increase in the diameter and the lumen space of seminiferous tubules with complete spermatogenic layers in mature and immature male rats. Treated immature female rats revealed significant (p≤0.05) increase of tertiary growing follicles and the number of uterine glands. In conclusion camel milk administration caused a positive impact on male rats reproductive functions and fertility and enhanced the puberty of both immature male and female rats.
Perceived Stress in Pandemic Disaster: A Case Study from India and Nepal

An attempt has been made to examine the existing qualitative literature on pandemic disaster and mental health in a holistic sense. From the collected data from respondents, it is true that there is some level of linkages between lockdown/isolation/pandemic disaster on stress and mental health. Stress, although it's a rampant gap between mind and reality, is adverse to human health if a person cannot manage it properly. Some people have stress endurance power where's some do not. In the time of COVID-19 lockdown, people of Nepal and India substantially in stressful condition which is worst for low income holder. Spiritual practices, physical exercises, use of book and entertainment channel and doing meditation and yoga are best therapy to check stressful condition. Otherwise, it can create psychosis problem moreover. Not only government but also family members play an important role in controlling the stress level of the family. In Asian countries like India and Nepal, the psychological problems are not taken in serious manner. Even there is lack of manpower in this field to deal the situation focusing on poor and low income community who are more vulnerable. Government need to provide the proper news and information to the citizens and family members need to get involved themselves in reading, writing, dancing, watching, exercising, counselling from experts are recommended by respondents. Making ourselves busy in different activities and events at home will obviously control stress at some level.
Designing Constructed Wetlands for Nitrogen Removal

Many constructed wetlands adequately treat BOD 5 , TSS, and bacteria. However, a review of nitrogen (N) data from 52 constructed and natural wetlands in the North American data base confirmed that N removal was variable. Nitrification and denitrification require aerobic and anaerobic conditions. This paper presents case histories of systems that use alternating shallow and deep water zones to create both environments. Regression analysis of N removal and N loadings in 18 shallow-deep water systems suggested that NH 4 + loading (kg N/ha/day) could be used to predict effluent NH 4 + values. Combinations of shallow water-emergent vegetation and deep water-submergent vegetation with low NH 4 + (and TKN) loading rates can produce very low levels of discharged NH 4 + .
Patterns of Treatment in Patients with Heart Failure with Preserved Ejection Fraction: the REasons for Geographic And Racial Differences in Stroke study

Purpose We described medication use patterns among REasons for Geographic And Racial Differences in Stroke (REGARDS) participants hospitalized for heart failure with preserved ejection fraction (HFpEF) (152 hospitalizations, 101 unique individuals). Methods Medication data were obtained from medical record review and Medicare Part D pharmacy claims. We compared discharge medication prescriptions between patients with and without chronic kidney disease (CKD), coronary heart disease (CHD), chronic obstructive pulmonary disease (COPD), and diabetes. Results The mean age was 74.8 years, 53.3% were black and 73.7% were female. Hypertension (97.2%), diabetes (65.1%), COPD (51.3%), CKD (41.1%) and history of CHD (60.9%) were common. On admission and discharge, respectively, beta-blockers (66.4%, 72.7%), angiotensin converting enzyme inhibitors or angiotensin receptor blockers (42.8%, 51.7%), diuretics (61.2%, 80.9%), loop diuretics (55.9%, 78.3%), calcium channel blockers (41.0%, 41.2%) and statins (44.7%, 50.3%) were commonly used. Spironolactone, digoxin, hydralazine plus isosorbide dinitrate (HISDN), isosorbide dinitrate alone and aldosterone receptor antagonists were used by <20%. For each medication, prescriptions were more common at discharge than admission. Many participants did not have Medicare claims for filled prescriptions in the year following discharge. A higher percentage of patients with versus without CKD, CHD, and diabetes had discharge prescriptions statins. Participants with CKD were also more likely to receive prescriptions for HISDN. Conclusion Beta-blockers and diuretics were commonly prescribed at admission and discharge among HFpEF, but pharmacy claims for these medications within one-year were substantially less common. The comorbidities CHD, CKD, and diabetes were associated with prescriptions of statins at discharge.
Effect of Freezing-thawing and Storage Time on Some Specific Human Enzymes

The present research was designed and conducted to study the effect of freezing-thawing and storage time on some specific human enzymes. The enzymes aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), creatine phosphokinase (CPK) and lactate dehydrogenase (LDH) were analysed immediately after sample collection, after undergoing freeze thaw at – 4°C, – 20°C and –70°C at day o and after 7 days of storage at – 4°C, – 20°C and – 70°C. A total of 50 healthy males and 50 healthy females were used for the study and sample collection was by pooled serum. Our results show that there was no statistically significant difference (p>0.05) between AST, ALT, ALP and CPK levels obtained after freeze-thaw at – 4°C, – 20°C and –70°C at day 0 when compared with the control for both males and females. Also, no statistically significant difference (p>0.05) was seen in the levels of AST, ALT, ALP, CPK analysed Original Research Article Ekweogu et al.; ARRB, 29(3): 1-6, 2018; Article no.ARRB. 44686 2 after 7 day storage at – 4°C, – 20°C and –70°C in both males and females when compared with the control. However, there was a significant difference (p<0.05) in the levels of LDH obtained after freeze-thaw at – 4°C both at day 0 and after 7 days of storage. In conclusion, the results showed that the specific enzymes studied were most stable when stored at –70°C for 7 days assuming sample analysis is not carried out shortly after sample collection.
Adhesion and subsequent biofilm formation of Candida albicans on chemically different surfaces as investigated using confocal scanning laser microscopy

Candida albicans comprises part o f the normal human flora whose growth is usually restricted by the normal flora bacteria and the host’s immune system. C albicans is an opportunistic fungal pathogen which causes infections in immunocompromised individuals, mechanical trauma victims, and iatrogenic patients. C. albicans can ingress the human host by adhering to a plastic surface (i.e., prosthetic devices, catheters, artificial organs, etc.) and forming a protective biofilm which provides a continuous reservoir of yeast to be hematogeneously dispersed. In order to battle device-related infections, the mechanisms o f adhesion and biofilm formation o f C. albicans must be recognized. A welldefined culture surface allows the initial adhesion and biofilm development to be studied. There has been some skepticism as to whether the initial adhesion events have any relationship to subsequent biofilm formation. Thus, to better comprehend the relationship between the initial adhesion rates and the long term growth rate and mature biofilm formation, these events were studied on two different culture surfaces, native polystyrene and Pluronic F 127-conditioned polystyrene. The adhesion studies determined that Pluronic F 127 adsorption dramatically reduced the adhesion o f two strains o f C. albicans o f different serotypes to polystyrene. The biofilm growth studies, analyzed by confocal scanning laser microscopy, revealed that Pluronic F127 decreased the biofilm surface coverage, cluster group size, thickness, and the presence o f hyphal elements over the untreated polystyrene. These findings indicate that the effect o f a material’s surface chemistry on the initial adhesion process has a direct influence on subsequent biofilm formation.
DETERMINANTS OF NEUTRALIZATION IN ENVELOPE PROTEINS OF HEPATITIS C VIRUS

ii ACKNOWLEDGMENTS. v LIST OF TABLES . vii LIST OF FIGURES . viii CHAPTER I: INTRODUCTION . 1 CHAPTER II: A HEPATITIS C VIRUS ENVELOPE POLYMORPHISM CONFERS RESISTANCE TO NEUTRALIZATION BY POLYCLONAL SERA AND BROADLY NEUTRALIZING MONOCLONAL ANTIBODIES . 11 ABSTRACT . 12 IMPORTANCE . 13 INTRODUCTION . 14 MATERIALS AND METHODS. 16 RESULTS . 23 DISCUSSION . 30 FIGURES . 33 CHAPTER III: AGREEMENT BETWEEN HEPATITIS C VIRUS NEUTRALIZATION MEASURED USING REPLICATION COMPETENT VIRUS AND PSEUDOPARTICLES . 49 ABSTRACT . 50 IMPORTANCE . 52 INTRODUCTION . 53 MATERIALS AND METHODS. 56 RESULTS . 62 DISCUSSION . 67 FIGURES . 73 CHAPTER IV: DISCUSSION . 88 APPENDIX REFERENCES . 92 CURRICULUM VITAE . 114
THE EFFECT OF TEMPERATURE AND METHOD OF DRYING ON ISOT (URFA PEPPER) AND ITS VITAMIN C DEGRADATION KINETICS

This study investigated drying and vitamin C degradation kinetics in isot (red peppers) at different temperatures (55, 65 and 75°C) and conditions (vacuum and hot air drying). The drying temperature and method had a significant effect on the loss of vitamin C. Vacuum dried samples at 55°C retained the highest quantity of vitamin C, while the samples dried at 75°C in a cabinet dryer lost the highest amount of vitamin C. The results showed that vitamin C is especially sensitive to the presence of oxygen and higher temperatures. The Weibull model was found to provide the mathematical equation best describing the ascorbic acid degradation kinetics in red peppers, while the Page model best reflected the drying kinetics.
High frequency regeneration from leaf derived callus and its histological studies in Lepianthes umbellata

ABSTRACT A protocol was standardized for callus initiation and shoots regeneration from leaf explants of Lepianthes umbellata. The explant was cultured on Murashige and Skoog (MS) medium supplemented with different concentrations and combinations of 2,4-Dichlorophenoxyacetic acid (2,4-D), 6-Benzylaminopurine (BAP), and 1-Naphthalene acetic acid (NAA) for shoot bud initiation and multiplication. High frequency of shoot regeneration and maximum number of shoots per explant were achieved on MS medium fortified with 0.5 mg L−1 NAA and 1.0 mg L−1 BAP. The elongations of shoots were achieved on the same medium supplemented with 1.0 mg L−1 Gibberelic acid (GA3), indole-3-acetic acid (IAA), and indole-3-butyric acid (IBA) at different concentrations on half strength MS medium were used for rooting of the micro shorts. Highest efficiency for rooting was observed on MS with 1.5 mg L−1 IBA. Regenerated plantlets were successfully transferred for acclimatization (70%). Histological studies showed that embryoids and shoot buds initiating from the callus masses, that is, indirect organogenesis. Cytological variations were observed in callus cultures.
Reduced barnacle larval abundance and settlement in response to large‐scale oceanic disturbances: Temporal patterns, nearshore thermal stratification, and potential mechanisms

We assessed the effects of large‐scale oceanic disturbances on the settlement rate of an abundant intertidal barnacle. Daily or weekly settlement, nearshore temperature, currents, and abundance of early‐stage barnacle nauplii and Chthamalus fissus cyprids were measured in La Jolla, California, from the inception of the large‐scale warm‐water anomaly known as the “Blob” in 2014, to 1 yr following the 2015/2016 El Niño. We also measured over 2 yr of weekly settlement rates during the 1997/1998 El Niño in La Jolla and in two Mexican sites. Settlement was low during the Blob and the 2015/2016 El Niño, but increased dramatically after its end, and rates remained high through spring 2017. Barnacle nauplii and C. fissus cyprid abundances were also low during the Blob and El Niño. Nearshore water column thermal stratification and variability of the high‐frequency cross‐shore currents, a measure of internal wave activity, declined during the Blob and El Niño, but increased at the end of El Niño. Similarly, settlement rates in the Mexican sites were low during the 1997/1998 El Niño. The reduction in settlement during the Blob and El Niño may be related to two factors: a decrease in water column stratification, which can influence internal bore larval transport and the cross‐shore distribution of larvae, and also to reduced early‐stage larval abundance, potentially related to lower reproductive output or high nauplii mortality during the disturbances.