Risk analysis and seroprevalence of bovine ephemeral fever virus in Punjab, Pakistan.

Bovine ephemeral fever (BEF) is a vector-borne viral disease caused by the RNA virus which belongs to the genus Ephemerovirus and the family Rhabdoviridae. To evaluate the effect of the risk factors like the breed of cattle and buffaloes, age, sex, lactation, housing and region on the bovine ephemeral fever virus (BEFV) prevalence, ELISA and virus neutralisation (VN) tests (n = 600) were performed for the BEFV prevalence. The seroprevalence in cattle was 45.6% and 42% by ELISA and VN, respectively (P = 0.001). The breed-wise seropositive ratio was (55-64%) in cattle and (22.5-18.3%) in buffaloes by VN and ELISA. The sex-wise prevalence was (40-49.4%) in females and (35.8-46%) in males by VN and ELISA in cattle and a similar prevalence was reported in buffaloes. The age-wise prevalence in bovines by ELISA was 5.33, 22.66 and 17.66% in the age group < 1 year, 1-3 years and > 3 years, respectively. The disease prevalence was higher in the age group of 1-3 years. The prevalence was higher during the 3rd lactation in bovines. The region-wise prevalence was higher in the 07 districts while lower (18-21%) in Rawalpindi District by VN and ELISA, respectively (P = 0.001). Commercial dairy farms of cattle showed a higher disease prevalence (52% and 44%) than non-commercial farms (38% and 36%) by ELISA and VN, respectively (P = 0.227). Exotic cows showed higher disease prevalence (76.67% and 70%) by ELISA and VN. The mortality in bovines was 5% (7.7% and 2.3%) in the cattle and buffaloes. The case fatality of BEFV in bovines was 12.25%. There was a significant effect of the risk factors like the breed, age, sex, lactation, housing and region on the BEFV prevalence. This is the first comprehensive study of BEFV in Pakistan.

Data of biomass and N in grass and clover roots, stubbles, and herbage and associated N2O and CO2 emissions, inclusive soil air composition, following autumn ploughing - A field study.

This article presents the detailed data of the soil characteristics, field management, amount and N content of below- (roots +crown) and aboveground (stubble and herbage) grass mixture, red clover and red clover grass swards at the end of the 3rd production year, together with fluxes of greenhouse gas emissions (N2O, CO2, CH4) and soil air composition (CO2, N2O, CH4, N2 and O2) of a field experiment in Norway. These data supplement the findings presented in the research article " Roots and other residues from ley with or without red clover: quality and effects on N2O Emission Factor in a partly frozen soil following autumn ploughing"(Bleken et al. 2022). For understanding of the effects of incorporating ley above- and belowground residues on cumulative greenhouse emissions refer to article from this research.

Roots and other residues from leys with or without red clover: Quality and effects on N2O emission factors in a partly frozen soil following autumn ploughing.

Revised IPCC guidelines assume that a constant share of N in decomposing crop residues is directly emitted as N2O (emission factor: EFN2O), and calculate the amount of nitrogen (N) in non-removable residues of temporary grasslands proportionally to the average annual herbage yield. However, EFN2O depends on the intrinsic quality of the residues and their interactions with environmental conditions. Only a few field studies on N2O emissions from grassland renewal are available, and none have simultaneously quantified the N amount and quality of non-removable residues (roots and stubble). To gain insight into the effect of non-removable residue quality on EFN2O, we studied the amount and quality of roots and stubble and their effect on EFN2O following the ploughing of three-year-old swards. The measured amount of N in non-removable residues was approximately 20, 25, and 31 kg N per 1 Mg average annual dry matter yield in grass, red clover-grass, and red clover, and 70-83% of it was below ground. However, the EFN2O of non-removable residues measured over 252 days was lower (0.24%, SE = 14% for grass and red clover-grass) than the IPCC default value (0.6%, CV: 50%) for wet regions, although within the uncertainty margin, and was significantly lower than the EFN2O of incorporated herbage, which was related to differences in EFCO2. We advocate for more specific studies that separate the effects of belowground and aboveground residues (AGR), considering the possibility of simplifying the accounting of N2O emissions from belowground residues while improving that of non-removable AGR from temporary grasslands and other green crops. We observed the accumulation of N2O in the frozen soil under snow, which was released during diurnal percolation of meltwater. N2O emissions from frozen soil accounted for 30% or more of the total emissions.

Association of Pyuria with Uropathogens in Young Children.

OBJECTIVE: To examine the association between uropathogens and pyuria in children <24 months of age. STUDY DESIGN: A retrospective study of children <24 months of age evaluated in the emergency department for suspected urinary tract infection (UTI) with paired urinalysis and urine culture during a 6-year period. Bagged urine specimens or urine culture growing mixed/multiple urogenital organisms were excluded. Analysis was limited to children with positive urine culture as defined by the American Academy of Pediatrics clinical practice guideline culture thresholds. RESULTS: Of 30 462 children, 1916 had microscopic urinalysis and positive urine culture. Urine was obtained by transurethral in-and-out catheterization in 98.3% of cases. Pyuria (≥5 white blood cells per high-powered field) and positive leukocyte esterase (small or more) on the urine dipstick were present in 1690 (88.2%) and 1692 (88.3%) of the children respectively. Children with non-Escherichia coli species were less likely to exhibit microscopic pyuria than children with E coli (OR 0.24, 95% CI 0.17-0.34) with more pronounced effect on Enterococcus and Klebsiella (OR 0.08, 95% CI 0.03-0.18 and OR 0.18, 95% CI 0.11-0.27 respectively). Similarly, positive leukocyte esterase was less frequently seen in non-E coli uropathogens compared with E coli. CONCLUSIONS: Pyuria and leukocyte esterase are not sensitive markers to identify non-E coli UTI in young children. More sensitive screening biomarkers are needed to identify UTI with these uropathogens.

Randomized trial of two maintenance doses of vitamin D in children with chronic kidney disease.

BACKGROUND: Correction of nutritional vitamin deficiency is recommended in children with chronic kidney disease (CKD). The optimal daily dose of vitamin D to achieve or maintain vitamin D sufficiency is unknown. METHODS: We conducted a phase III, double-blind, randomized trial of two doses of vitamin D3 in children ≥ 9 years of age with CKD stages 3-5 or kidney transplant recipients. Patients were randomized to 1000 IU or 4000 IU of daily vitamin D3 orally. We measured 25-hydroxvitamin D (25(OH)D) levels at baseline, 3 months and 6 months. The primary efficacy outcome was the percentage of patients who were vitamin D replete (25(OH)D ≥ 30 ng/mL) at 6 months. RESULTS: Ninety-eight patients were enrolled: 49 randomized into each group. Eighty (81.6%) patients completed the study and were analyzed. Baseline plasma 25(OH)D levels were ≥ 30 ng/mL in 12 (35.3%) and 12 (27.3%) patients in the 1000 IU and 4000 IU treatment groups, respectively. At 6 months, plasma 25(OH)D levels were ≥ 30 ng/mL in 33.3% (95% CI: 18.0-51.8%) and 74.4% (95% CI: 58.8-86.5%) in the 1000 IU and 4000 IU treatment groups, respectively (p = 0.0008). None of the patients developed vitamin D toxicity or hypercalcemia. CONCLUSIONS: In children with CKD, 1000 IU of daily vitamin D3 is unlikely to achieve or maintain a plasma 25(OH)D ≥ 30 ng/mL. In children with CKD stages 3-5, a dose of vitamin D3 4000 IU daily was effective in achieving or maintaining vitamin D sufficiency. CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT01909115.

Pyuria and Urine Concentration for Identifying Urinary Tract Infection in Young Children.

OBJECTIVES: Accuracy of pyuria for urinary tract infection (UTI) varies with urine concentration. Our objective of this study was to determine the optimal white blood cell (WBC) cutoff for UTI in young children at different urine concentrations as measured by urine specific gravity. METHODS: Retrospective cross-sectional study of children <24 months of age evaluated in the emergency department for suspected UTI with paired urinalysis and urine culture during a 6-year period. The primary outcome was positive urine culture result as described in the American Academy of Pediatrics clinical practice guideline culture thresholds. Test characteristics for microscopic pyuria cut points and positive leukocyte esterase (LE) were calculated across 3 urine specific gravity groups: low <1.011, moderate 1.011 to 1.020, and high >1.020. RESULTS: Of the total 24 171 patients analyzed, urine culture result was positive in 2003 (8.3%). Urine was obtained by transurethral in-and-out catheterization in 97.9%. Optimal WBC cutoffs per high-power field (HPF) were 3 (positive likelihood ratio [LR+] 10.5; negative likelihood ratio [LR-] 0.12) at low, 6 (LR+ 12; LR- 0.14) at moderate, and 8 (LR+ 11.1; LR- 0.35) at high urine concentrations. Likelihood ratios for small positive LE from low to high urine concentrations (LR+ 25.2, LR- 0.12; LR+ 33.1, LR- 0.15; LR+ 37.6, LR- 0.41) remained excellent. CONCLUSIONS: Optimal pyuria cut point in predicting positive urine culture results changes with urine concentration in young children. Pyuria thresholds of 3 WBCs per HPF at low urine concentrations whereas 8 WBCs per HPF at high urine concentrations have optimal predictive value for UTI. Positive LE is a strong predictor of UTI regardless of urine concentration.

Connotations of psychological and physiological health in the psychosocial work environment: An industrial context.

BACKGROUND: Psychological conditions are experiences of the conscious and unconscious elements of the work context, which revolve around workers' perceptions of feeling either engaged or disengaged with the assigned tasks. In the psychosocial work environment of hazardous industries like petrochemicals where production lasts twenty-four hours a day and continues seven-days-a-week, a psychologically available worker is extremely important. Psychological availability refers to when workers who are physically, emotionally and psychologically engaged at the moment of performing tasks. OBJECTIVE: The broad objective of this study was to investigate the direct and indirect effects of behavioral factors on the psychological and physiological health of workers. METHODS: The latest, second generation technique, which is structural equation modeling, is used to identify the relationships between behavioral antecedents and health outcomes. A total of 277 technical workers participated, aged between 20 and 49 and were healthy in all aspects. RESULTS: The study results showed quantitative demands, emotional demands, work-family conflict, and job insecurity were significantly associated with both psychological (stress) and physiological (Body Mass Index) factors. The social support of colleagues produced mixed findings with direct and indirect paths. Stress also significantly mediates the psychosocial factors and burnout of the workers. CONCLUSION: The study concluded that workers were physically available, but they experienced distractions as members of social systems, affecting their physiological and psychological health.

Variation in genotoxic susceptibility and biomarker responses in Cirrhinus mrigala and Catla catla from different ecological niches of the Chenab River.

A large number of methods have been applied to evaluate genotoxic damage in different aquatic species. Comet assay, as a method for detecting DNA alterations, and micronucleus test, as an index of chromosomal damage are the most widely used and authentic methods in laboratory and field studies. The primary objective of the study was to evaluate the genotoxic effects of heavy metals generated by toxic industrial effluents and various kinds of pollutants from urban and agricultural areas and domestic waste on Catla catla and Cirrhinus mrigala due to water pollution in the Chenab River, Pakistan. The heavy metals Cd, Cu, Mn. Zn, Pb, Cr, Sn, and Hg were detected by atomic absorption spectrophotometry from water samples collected from predetermined sampling sites. All the physicochemical parameters and heavy metals were found to exceed the upper limits recommended by various agencies. Comet assays showed significant (p < 0.05) DNA damage in C. mrigala compared to C. catla for tail length and olive tail moment from three different sites. Significant (p < 0.05) differences were reported between fish collected from polluted sites and farmed fish, but only non-significant (p > 0.05) findings were observed between fish collected from farmed and non-polluted upstream waters. Micronucleus assays showed similar findings for single and double micronucleus induction in C. catla and C. mrigala. A significantly (p < 0.05) higher micronuclei induction and percent tail DNA was observed in C. mrigala specimen collected from the polluted site. These findings infer that DNA damage could be used as a biomarker of pollution load and its early monitoring by using simple and reliable techniques such as the comet and micronucleus assays, expedient methods for toxicity screening of aquatic environments. Regular monitoring is necessary to assess eco-health of the Chenab River by choosing perhaps C. mrigala, being a bottom feeder, as a bioindicator that could provide more reliable information to determine the status of the environmental quality of the river.

First report on fish cysteine as a biomarker of contamination in the River Chenab, Pakistan.

The eastern and southern parts of the Faisalabad city produce considerable quantities of industrial and municipal pollutants, much of which is drained into the River Chenab, reducing the productivity of fauna and flora in the river. This study was aimed to determine whether cysteine is useful as a biomarker of exposure to polluted fresh water. The amino acid profile of fish muscle was analyzed by paper chromatography in Cirrhinus mrigala and Labeo rohita from the River Chenab to determine habitat related variations due to the pollution from industrial and domestic sources. C. mrigala showed higher level of metal contamination in muscle tissues for Sn, Cr, Pb, Zn, Mn, Cu, and Cd when compared to L. rohita. Both fish species collected from polluted areas of the river Chenab showed significantly (P < 0.01) higher levels of metals in comparison to upstream and farmed fish. Farmed C. mrigala showed cysteine concentrations in the muscle tissue as 22 ± 1 mg/g dry weight, but concentrations increased to 45 ± 2 mg/g dry weight for fish from a mildly polluted section of the river, and further increased to 83 ± 2 mg/g dry weight in more heavily polluted sections. Cysteine concentration in farmed L. rohita was detected as 28 ± 2 and 25 ± 4 mg/g dry weight, respectively for farmed fish and fish from a mildly polluted section of the river, and then increased to 94 ± 3 mg/g dry weight for fish from highly polluted water. C. mrigala from a mildly polluted area of the river also had higher levels of cysteine in the muscle, along with increases in aspartic acid, glutamic acid, and alanine. Elevated concentrations of cysteine seem to be associated with a threat to these fish species in polluted sections of the river, and thus may be used as a biomarker.

High-Resolution Denitrification Kinetics in Pasture Soils Link N2O Emissions to pH, and Denitrification to C Mineralization.

Denitrification in pasture soils is mediated by microbial and physicochemical processes leading to nitrogen loss through the emission of N2O and N2. It is known that N2O reduction to N2 is impaired by low soil pH yet controversy remains as inconsistent use of soil pH measurement methods by researchers, and differences in analytical methods between studies, undermine direct comparison of results. In addition, the link between denitrification and N2O emissions in response to carbon (C) mineralization and pH in different pasture soils is still not well described. We hypothesized that potential denitrification rate and aerobic respiration rate would be positively associated with soils. This relationship was predicted to be more robust when a high resolution analysis is performed as opposed to a single time point comparison. We tested this by characterizing 13 different temperate pasture soils from northern and southern hemispheres sites (Ireland and New Zealand) using a fully automated-high-resolution GC detection system that allowed us to detect a wide range of gas emissions simultaneously. We also compared the impact of using different extractants for determining pH on our conclusions. In all pH measurements, soil pH was strongly and negatively associated with both N2O production index (IN2O) and N2O/(N2O+N2) product ratio. Furthermore, emission kinetics across all soils revealed that the denitrification rates under anoxic conditions (NO+N2O+N2 µmol N/h/vial) were significantly associated with C mineralization (CO2 µmol/h/vial) measured both under oxic (r2 = 0.62, p = 0.0015) and anoxic (r2 = 0.89, p<0.0001) conditions.

Renin Angiotensin System Blocker Fetopathy: A Midwest Pediatric Nephrology Consortium Report.

OBJECTIVES: Fetuses continue to be exposed to renin angiotensin system (RAS) blockers despite their known teratogenicity and a black box warning. We hypothesized that fetopathy from in utero exposure to RAS blockers has a broader spectrum of clinical manifestations than described previously and that there are a variety of clinical scenarios leading to such exposures. STUDY DESIGN: This was a retrospective study performed through the Midwest Pediatric Nephrology Consortium. Cases of RAS blocker fetopathy were identified, with determination of renal and extrarenal manifestations, timing of exposure, and the explanation for the fetal exposure. RESULTS: Twenty-four cases were identified. RAS blocker exposure after the first trimester was associated with more severe renal manifestations. Chronic dialysis or kidney transplantation was required in 8 of 17 (47%) patients with RAS blocker exposure after the first trimester and 0 of 7 patients with exposure restricted to the first trimester (P = .05). Extrarenal manifestations, some not previously noted in the literature, included central nervous system anomalies (cystic encephalomalacia, cortical blindness, sensorineural hearing loss, arachnoid cysts) and pulmonary complications (pneumothorax, pneumomediastinum). RAS blocker exposure usually was secondary to absent or poor prenatal care or undiagnosed pregnancy. CONCLUSION: RAS blocker fetopathy continues to be a cause of considerable morbidity, with more severe renal manifestations associated with exposure after the first trimester. A variety of significant extrarenal manifestations occur in these patients. Clinicians should emphasize the risk of fetopathy when prescribing RAS blockers to women of childbearing age.

Aliskiren, the first direct renin inhibitor: assessing a role in pediatric hypertension and kidney diseases.

This article provides a review of the role of aliskiren, a direct renin inhibitor, in pediatric hypertension and kidney diseases. Among the many mechanisms involved in regulating blood pressure, the renin-angiotensin-aldosterone system (RAAS) plays a major role. Additionally, the RAAS has been identified as a contributing factor to cardiovascular and renal diseases for more than three decades. The potential benefits of inhibiting the RAAS by aliskiren alone or in combination with other RAAS blockers (ACEIs, ARBs) seem to be theoretically promising. However, caution should be exercised in treating children, especially in those with significant chronic kidney disease until there is more evidence regarding the safety and efficacy of this new drug in the pediatric population from ongoing clinical trials.

Domain wise docking analyses of the modular chitin binding protein CBP50 from Bacillus thuringiensis serovar konkukian S4.

This paper presents an in silico characterization of the chitin binding protein CBP50 from B. thuringiensis serovar konkukian S4 through homology modeling and molecular docking. The CBP50 has shown a modular structure containing an N-terminal CBM33 domain, two consecutive fibronectin-III (Fn-III) like domains and a C-terminal CBM5 domain. The protein presented a unique modular structure which could not be modeled using ordinary procedures. So, domain wise modeling using MODELLER and docking analyses using Autodock Vina were performed. The best conformation for each domain was selected using standard procedure. It was revealed that four amino acid residues Glu-71, Ser-74, Glu-76 and Gln-90 from N-terminal domain are involved in protein-substrate interaction. Similarly, amino acid residues Trp-20, Asn-21, Ser-23 and Val-30 of Fn-III like domains and Glu-15, Ala-17, Ser-18 and Leu-35 of C-terminal domain were involved in substrate binding. Site-directed mutagenesis of these proposed amino acid residues in future will elucidate the key amino acids involved in chitin binding activity of CBP50 protein.

Three dimensional (3D) structure prediction and substrate-protein interaction study of the chitin binding protein CBP24 from B. thuringiensis.

Bacillus thuringiensis is an insecticidal bacterium whose chitinolytic system has been exploited to improve insect resistance in crops. In the present study, we studied the CBP24 from B. thuringiensis using homology modeling and molecular docking. The primary and secondary structure analyses showed CBP24 is a positively charged protein and contains single domain that belongs to family CBM33. The 3D model after refinement was used to explore the chitin binding characteristics of CBP24 using AUTODOCK. The docking analyses have shown that the surface exposed hydrophilic amino acid residues Thr-103, Lys-112 and Ser-162 interact with substrate through H-bonding. While, the amino acids resides Glu-39, Tyr-46, Ser-104 and Asn-109 were shown to have polar interactions with the substrate. The binding energy values evaluation of docking depicts a stable intermolecular conformation of the docked complex. The functional characterization of the CBP24 will elucidate the substrate-interaction pathway of the protein in specific and the carbohydrate binding proteins in general leading towards the exploration and exploitation of the prokaryotic substrate utilization pathways.

The significance of early accumulation of nanomolar concentrations of NO as an inducer of denitrification.

Denitrifying bacteria have variable ability to perform efficient and balanced denitrification during oxygen depletion. NO is often assumed to exert a positive feedback in the transcription of denitrification genes, because NO-dependent activators have been identified. The regulatory network of denitrification is complex, however, and the significance of NO signalling needs to be studied in vivo. We utilized acetylene-catalysed NO oxidation to scavenge NO produced by batch cultures of denitrifying bacteria during transition from oxic to anoxic respiration, to explore the effects on the kinetics of NO, N(2) O and N(2) production. The results demonstrated that nanomolar concentrations of NO accumulating prior to complete depletion of oxygen exert a significant positive feedback on the initiation of denitrification in Paracoccus denitrificans. The early NO signal appeared essential to minimize the transient accumulation of NO during the subsequent anoxic phase for Agrobacterium tumefaciens, but not for P. denitrificans and Pseudomonas aureofaciens. In summary, the results indicate that the early accumulation of nanomolar concentrations of NO has a significant, but strain-dependent effect on the expression of denitrification.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

UNLABELLED: RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. AVAILABILITY: http://www.cemb.edu.pk/sw.html ABBREVIATIONS: RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.