Publications by authors named "Farah Khan"

115 Publications

Sirolimus loaded chitosan functionalized poly (lactic-co-glycolic acid) (PLGA) nanoparticles for potential treatment of age-related macular degeneration.

Int J Biol Macromol 2021 Sep 15. Epub 2021 Sep 15.

Department of Pharmaceutics, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi 110062, India. Electronic address:

The usefulness of sirolimus (SIR) in the treatment of diseases that involve retinal degeneration like age-related macular degeneration (AMD) has been well documented. However, the problem still remains probably owing to the peculiar environment of the eye and/or unfavourable physiochemical profile of SIR. In the present work, we aimed to fabricate sirolimus loaded PLGA nanoparticles (SIR-PLGA-NP) and chitosan decorated PLGA nanoparticles (SIR-CH-PLGA-NP) to be administered via non-invasive subconjunctival route. Both the nanoparticles were characterized in terms of size, zeta potential, DSC, FTIR and XRD analysis. Quality by Design (QbD) approach was employed during the preparation of nanoparticles and the presence of chitosan coating was confirmed through thermogravimetric analysis and contact angle studies. Cationic polymer modification showed sustained in-vitro SIR release and enhanced ex-vivo scleral permeation and penetration. Further, SIR-CH-PLGA-NP revealed enhanced cellular uptake and thus, reduced lipopolysaccharide (LPS)-induced free-radicals generation by RAW 264.7 cells. The prepared nanoparticles were devoid of residual solvent and were found to be safe in HET-CAM analysis, RBCs damage analysis and histopathology studies. Moreover, high anti-angiogenic potential was observed in SIR-CH-PLGA-NP compared with SIR-PLGA-NP in chorioallantoic membrane (CAM) test. Overall, the current work opens up an avenue for further investigation of CH-PLGA-NP as SIR nanocarrier in the treatment of AMD.
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http://dx.doi.org/10.1016/j.ijbiomac.2021.09.069DOI Listing
September 2021

Morphological and palynological assessment of taxonomically problematic genus Paspalum based on light and scanning electron microscopy.

Microsc Res Tech 2021 Sep 16. Epub 2021 Sep 16.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

Present research work was carried out to clarify the variations among species of genus Paspalum morphologically and palynologically as this genus is taxonomically difficult due to having multiple similar morphologically overlapping characters which make it difficult to identify. Henceforth present research work was carried out to delimit taxa within the same genus by morphological and palynological tools through light microscopy (LM) and scanning electron microscopy (SEM). Both these tools are considered as the most useful taxonomic characters for taxonomically problematic genera. The results showed a lot of variations among morphological characters. In Paspalum dilatatum, the upper glume was ovate whereas in the other two species, the upper glume was elliptic. The upper glume apex found in P. dilatatum and Paspalum scrobiculatum was obtuse whereas in Paspalum distichum, upper glume apex was acute. Glume nerves showed variation in all three species. Paspalum distichum was 3 nerved, P. scrobiculatum was 5-7 nerved, and P. dilatatum was 5-9 nerved. All three species showed variation in lemma nerves. Paspalum scrobiculatum had 3 nerved lemma whereas in P. distichum 3-5 nerved and P. dilatatum 5-9 nerved lemma were present. In polar and equatorial view, pollen grains ranged from 25 (20-30) to 37.5 (30-45) μm. Paspalum distichum appeared to be the smallest in size whereas P. dilatatum was the largest. Exine thickness ranged from 0.75 (0.5-1) to 1.35 (1.2-1.5) μm. The higher value of pollen fertility was found in P. scrobiculatum as 87.69% and the lowest value was in P. distichum as 78.08%. Morphological keys were also given for correct identification.
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http://dx.doi.org/10.1002/jemt.23936DOI Listing
September 2021

Morphological and palynological assessment of some taxa of genus Echinochloa through light and scanning electron microscopy.

Microsc Res Tech 2021 Aug 5. Epub 2021 Aug 5.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

The present study was undertaken to gather information on selected species of Echinochloa based on their morphological and palyonological examination through light and scanning electron microscopy. As the Echinochloa species are most problematic grass weeds and exhibit high interspecific and intraspecific variability so due to their great morphological diversity it is difficult to recognize them. A lot of variation was observed in morphological features of studied taxa. In the present study, E. colona had more or less spreading dense racemes whereas in E. crus-galli racemes were linear to ovate. Upper glume surface was pubescent in E. colona, hispid in E. crus-galli and spinose in E. walteri. E. colona was comprised of five-nerved glumes whereas in E. crus-galli glumes were three-nerved. Although pollen basic characters in family Poaceae remains consistent but great variation was observed in pollen of studied taxa. The pollen size was quite variable among the species of genus Echinochloa. In polar view, the size of pollen grains ranged from 27.5 (20-35) μm to 40 (30-50) μm. E. crus-galli was appeared to be the smallest in size whereas E. colona was the largest.). P/E ratio ranged from 0.84 to 1.15 μm among the species. The highest value of pollen fertility was found in E. colona as 93.33% and lowest was in E. crus-galli as 87.50%. The morphological key of studied taxa is also given to study variations. In conclusion, it was observed that microscopy of morphological and palynological assessment can play a vital role in identification of taxonomically problematic taxa.
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http://dx.doi.org/10.1002/jemt.23846DOI Listing
August 2021

Microbes in gynecologic cancers: Causes or consequences and therapeutic potential.

Semin Cancer Biol 2021 Jul 22. Epub 2021 Jul 22.

Division of Gynecology Oncology, Women's Health Services, Henry Ford Hospital, Detroit, MI, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA. Electronic address:

Gynecologic cancers, starting in the reproductive organs of females, include cancer of cervix, endometrium, ovary commonly and vagina and vulva rarely. The changes in the composition of microbiome in gut and vagina affect immune and metabolic signaling of the host cells resulting in chronic inflammation, angiogenesis, cellular proliferation, genome instability, epithelial barrier breach and metabolic dysregulation that may lead to the onset or aggravated progression of gynecologic cancers. While microbiome in gynecologic cancers is just at horizon, certain significant microbiome signature associations have been found. Cervical cancer is accompanied with high loads of human papillomavirus, Fusobacteria and Sneathia species; endometrial cancer is reported to have presence of Atopobium vaginae and Porphyromonas species and significantly elevated levels of Proteobacteria and Firmicutes phylum bacteria, with Chlamydia trachomatis, Lactobacillus and Mycobacterium reported in ovarian cancer. Balancing microbiome composition in gynecologic cancers has the potential to be used as a therapeutic target. For example, the Lactobacillus species may play an important role in blocking adhesions of incursive pathogens to vaginal epithelium by lowering the pH, producing bacteriocins and employing competitive exclusions. The optimum or personalized balance of the microbiota can be maintained using pre- and probiotics, and fecal microbiota transplantations loaded with specific bacteria. Current evidence strongly suggest that a healthy microbiome can train and trigger the body's immune response to attack various gynecologic cancers. Furthermore, microbiome modulations can potentially contribute to improvements in immuno-oncology therapies.
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http://dx.doi.org/10.1016/j.semcancer.2021.07.013DOI Listing
July 2021

Exploring Reproductive Health Impact of COVID 19 pandemic: In Depth Interviews with key stakeholders in Pakistan.

Pak J Med Sci 2021 Jul-Aug;37(4):1069-1074

Dr. Nusrat Shah Professor OBGYN - DUHS, Civil Hospital, Karachi, Pakistan.

Objective: To explore the effects of COVID 19 on reproductive and child health services and gender relations.

Methods: This is a Qualitative Exploratory Research. Due to lockdown, setting was online interviews on Zoom. Sampling was purposive. Five in-depth interviews were conducted in June 2020 followed by compilation of results and manuscript writing in July and August 2020.

Results: Maternal Neonatal morbidity and mortality will rise as part of collateral damage of C19. As all routine services of maternity care, family planning, post abortion care and vaccination were also in lockdown. Baby boom, unwanted pregnancies, unsafe abortions and violence against women will be the secondary consequences of C19.

Conclusion: Some critical services should never stop which include maternal and neonatal essential services. MNCH service continuity has to be maintained to optimize maternal neonatal health, prevent unwanted pregnancy and abortion. With appropriate standard operating procedures, and protective equipments, health facilities need to open. LHWs and community mobilisers with PPEs should continue services.
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http://dx.doi.org/10.12669/pjms.37.4.3877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8281157PMC
November 2020

Micro morphological foliar taxonomic studies of genus Paspalum based on scanning electron microscopy.

Microsc Res Tech 2021 Jul 2. Epub 2021 Jul 2.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

Paspalum is one of the 10 largest genera in Poaceae and is considered as a complex and taxonomically difficult genus due to its similar morphological characters within the species which makes it difficult to delimit taxa within the same genus. The current research work establishes the distinction among species of this genus and resolves taxonomic confusions among this genus. And this distinction is done by micro morphological foliar anatomical characterization by light and scanning electron microscopy. Both the abaxial and adaxial epidermal cuticles of three different species of genus Paspalum were studied and their phytoliths were observed through elemental dispersive spectrophotometric analysis by SEM first time in Pakistan. Results showed great variation in studied anatomical features. P. dilatatum Poir. was comprised of macro-hairs in the intercostal regions only whereas no macro-hairs were found in P. distichum Linn. and P. scrobiculatum Linn. Beak-shaped prickles were found in the intercostal regions on adaxial surface only in P. distichum Linn. and P. scrobiculatum Linn. whereas in P. dilatatum Poir., knife-shaped prickles were present in intercostal regions only on both abaxial and adaxial surfaces of leaf epidermis. No papillae were seen in P. dilatatum Poir whereas in P. distichum Linn. and P. scrobiculatum Linn. papillae were found abundantly. In genus paspalum, P. dilatatum Poir. phytoliths showed lowest mass percentage of silicon as 15.13% whereas P. distichum Linn. phytoliths showed highest mass percentage of silicon as 22.00%. Based on micro morphological foliar characteristics a taxonomic key of studied species is also provided to delimit the taxa.
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http://dx.doi.org/10.1002/jemt.23862DOI Listing
July 2021

Light and scanning electron microscopic study of genus Echinochloa species inhabited in Pakistan.

Microsc Res Tech 2021 Oct 20;84(10):2286-2290. Epub 2021 Apr 20.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

Grass taxonomy is quite problematic and insignificant taxonomic work has been done on Echinochloa with special reference to Pakistan. Therefore, the present study was carried out to provide taxonomic keys for the identification of this genus through microscopic epidermal leaf anatomical parameters. Light microscopy and scanning electron microscopy were done to delimit the different species. Special structures like hook cells, short and long cells, stomata, macro- and micro-hairs, prickles and silica bodies showed a lot of variation among each species. For instance, E. frumentacea can be distinguished from E. walteri by the presence of macro hairs between the veins. Furthermore, E. crus-galli can be distinguished from E. frumentacea in terms of macro hair size, that is, 45-60 μm and 20-60 μm, respectively. Similarly, E. colona showed marked variations in terms of prickles abundance from E. frumentacea. Overall results of this research reports valuable qualitative and quantitative diagnostic futures for the genus Echinochloa.
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http://dx.doi.org/10.1002/jemt.23782DOI Listing
October 2021

Oral Nigella sativa oil administration alleviates arsenic-induced redox imbalance, DNA damage, and metabolic and histological alterations in rat liver.

Environ Sci Pollut Res Int 2021 Aug 30;28(30):41464-41478. Epub 2021 Mar 30.

Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P., 202002, India.

Arsenic, an omnipresent environmental contaminant, is regarded as a potent hepatotoxin. Nigella sativa oil (NSO) consumption has been shown to improve hepatic functions in various in vivo models of acute hepatic injury. The present study evaluates the protective efficacy of NSO against sodium arsenate (As)-induced deleterious alterations in the liver. Male Wistar rats were divided into four groups, namely, control, As, NSO, and AsNSO. After pre-treating rats in AsNSO and NSO groups with NSO (2 mL/kg bwt, orally) for 14 days, NSO treatment was further extended for 30 days, with and without As treatment (5 mg/kg bwt, orally), respectively. As induced an upsurge in serum ALT and AST activities indicating liver injury, as also confirmed by the histopathological findings. As caused significant alterations in the activities of membrane marker enzymes and carbohydrate metabolic enzymes, and in the vital components of antioxidant defense system. Marked DNA damage and hepatic arsenic accumulation were also observed in As-treated rats. Oral NSO administration ameliorated these deleterious alterations and improved overall hepatic antioxidant and metabolic status in As-treated rats. Prevention of oxidative damage could be the underlying mechanism of NSO-mediated protective effects. The results suggest that NSO could be a useful dietary supplement in the management of arsenic hepatotoxicity.
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http://dx.doi.org/10.1007/s11356-021-13493-6DOI Listing
August 2021

Pollen morphological assessment of specific selected species of district Sheikhupura, Punjab, Pakistan under LM and SEM.

Microsc Res Tech 2021 May 31;84(5):955-966. Epub 2020 Dec 31.

Department of Botany, Lahore College for Women University, Jail Road Lahore, Pakistan.

Around 30 pollen samples, 16 families and 25 genera that were gathered, identified and preserved from 6 different localities of District Sheikhupura. Light and scanning electron microscopy was done for all collected flora. Out of the total samples, 43% specie was identified as herbs, 23% as shrubs, and 33% were identified as trees. The flora was both wild and cultivated. Wild plants were 33%, cultivated 40% and 26% of them were both wild and cultivated. Qualitative and Quantitative survey of pollens revealed polar shape of pollens were 37% spheroidal, 20% prolate spheroidal, 17% oblate spheroidal, remaining were rectangular and pecolpate. Sexine and nexine were available in 100% of samples. Thirty-three percentage of pollen grains were having spines on them. The presence of spines on pollen grains represents the evolutionary relationship amongst the plants. Current study was conducted to record and analyze palynomorphic diversity in district Sheikhupura, Punjab, Pakistan.
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http://dx.doi.org/10.1002/jemt.23656DOI Listing
May 2021

Application of multimicroscopic techniques (LM and SEM) in comparative palynological study of Asteroideae members, inhabited in Pakistan.

Microsc Res Tech 2021 May 17;84(5):1063-1077. Epub 2020 Dec 17.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

In the present study light and scanning electron microscopic approaches were used to study the palynological variations among 30 Asteroideae members. Variety of qualitative and quantitative palynological characters like pollen shape and type, pollen sculpturing, pollen size, P/E ratio, exine and intine thickness, interspecific difference, colpi size, pore size, spines length, spine width, and pollen fertility were observed. Results reported remarkable variations among pollen characters of studied taxa. The shape of pollen grains in polar and equatorial views varied from specie to specie such as spheroidal, prolate, oblate, subspheroidal, oblate spheroidal, prolate spheroidal, suboblate, and sub prolate. Bidens pilosa L. showed maximum pollen size in both polar and equatorial views, whereas minimum pollen size in polar view was found in Tetraneuris scaposa (DC.) Greene. (i.e., 30.5 μm) and in equatorial view was found in Cosmos sulphureus Cav. (25.5 μm).The highest P/E ratio (1.39 μm) was measured in Glebionis coronaria L. The values of exine and intine thickness also varied. Tricolporate, tetracolporate, trizonocolporate, pentoporate, and polypentoporate pollen types were examined. Spinateand echinate pollen sculpturingobserved under SEM. Variations in spine length and width also recorded. The maximum pollen fertility (98%) was measured in Chrysanthemum morifolium Ramat. and the lowest (56%) was recorded in Thymophylla tenuiloba (DC.) Small. It was concluded that the variations in qualitative and quantitative characters were seemed to be valuable for the taxonomic investigations of Asteroideae taxa.
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http://dx.doi.org/10.1002/jemt.23667DOI Listing
May 2021

Differentially expressed circulating microRNAs associated with idiopathic recurrent pregnancy loss.

Gene 2021 Feb 2;768:145334. Epub 2020 Dec 2.

College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates; Faculty of Sciences, El Manar University, Tunis, Tunisia.

Recurrent pregnancy loss (RPL) is a major pregnancy complication which reportedly affects 2-3% of all pregnancies. Currently, RPL lacks an effective therapy and a reliable diagnostic and prognostic biomarker. Circulating microRNAs were recently described as potential biomarkers of pregnancy-associated complications. The aim of this study was to determine microRNA expression patterns in the plasma of RPL patients as potential early biomarker of RPL. Study subjects comprised 20 women with early RPL (miscarriage at 8-12 weeks of gestation), and 20 age- and gestation-matched multiparous control women. Circulating microRNAs were extracted from maternal plasma, and the differential microRNA expression were determined using customized pathway-focused miRNA profiler kit. Of the 10 differentially-expressed microRNAs identified, Hsa-let-7e, Hsa-miR-221-3p, Hsa-miR-16, Hsa-miR-519d, Hsa-miR-184, Hsa-miR-410 were upregulated, while Hsa-miR-21, Hsa-miR-125, Hsa-let-7a, Hsa-let-7d were downregulated in RPL cases as compared to control women. Of these, 5 novel microRNAs were reported for the first time to be associated with RPL. These comprised Hsa-let-7e, Hsa-miR-519d, Hsa-miR-410 which were upregulated, and Hsa-let-7a, Hsa-let-7d which were downregulated in RPL. While its association with RPL was reported earlier, this study is also the first to report on the upregulation of Hsa-miR-184 in circulating fluids in association with RPL. The study provides for understanding circulating microRNAs expression pattern in RPL which may be involved in its pathogenesis and demonstrates their potential role as noninvasive diagnostic and prognostic biomarkers for RPL.
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http://dx.doi.org/10.1016/j.gene.2020.145334DOI Listing
February 2021

Scanning Electron Microscopy-based palynological characterization of selected Euphorbiaceae taxa colonized in Pakistan.

Microsc Res Tech 2021 May 18;84(5):850-859. Epub 2020 Nov 18.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

The present study was carried out on scanning electron microscopic-based palynological characterization of selected 20 Euphorbiaceae taxa. In this study, important pollen qualitative and quantitative features of selected Euphorbiaceae species such as polar diameter, equatorial diameter, P/E ratio, sculpturing of pollen, exine thickness, intine thickness, presence or absence of colpi and length of colpi, and pollen fertility were examined. Remarkable variations in these pollen characters had been observed among these species. In both polar and equatorial views, Riccinus communis L. exhibited the highest pollen size (polar = 264.1 μm, Equatorial = 270 μm), while Acalypha wilkesiana Mull Arg. showed lowest pollen size (Polar = 17 μm, Equatorial = 18.5 μm). Most of the pollen varied from oblate to spheroidal in shape. With regard to the P/E ratio, Sapium sebiferum L. Roxb showed the highest ratio while Bischofia javanica Blume showed minimum, that is, 1.18 and 0.85, respectively. Intine and exine thickness also varied. Most of the pollen grains were monade. Tricolporate, tricolpate, monocolpate, pentaporate, and polyporate pollen aperture types have been observed. Most of the plants showed regular, reticulate, and echinate pollen sculpturing. Pollen fertility also varied from species to species but most of the plant showed pollen fertility between 70 and 80%. Through this work, it has been concluded that quantitative and qualitative pollen features are helpful at the specific level as well as the generic level and can provide a fruitful taxonomic solution.
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http://dx.doi.org/10.1002/jemt.23644DOI Listing
May 2021

Scanning electron microscopic screening; Can it be a taxonomic tool for identification of traditional therapeutic plants.

Microsc Res Tech 2021 Apr 30;84(4):730-745. Epub 2020 Oct 30.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

The limiting factor in the utilization of herbal medicine is the risk of replacement or substitution of their plant resources. Therefore, the authentication of medicinal plants before its use in herbal medicines is essentially required. Hence, the prime objective of this study was to provide some reliable morpho-anatomical and morpho-palynological tools for the identification of nine traditional therapeutic plants of district Lahore. For this study, scanning electron microscopic and light microscopic approaches has been employed. Results reported great variations in qualitative and quantitative morpho-anatomical features of the epidermal cell, stomatal complexes, trichomes, silica bodies and oil droplets. For example, Aegle marmelos L. can be distinguished from Cestrum diurnum L. based on epidermal cell shapes, as irregular cells in former and lobed cells shape in later one. Similarly unicellular, bicellular, and multicellular trichomes could be an identification basis for Cynodon dactylon L., Lantana camara L., and Pongamia pinnata L., respectively. In combination with these morpho-anatomical characters, SEM-based morpho-palynological characterization also reported diagnostic value. Both the Aegle marmelos and Lantana camara possessed similar cell shape (irregular) but can be delimited based on their pollen morphology as spheroidal pollen was reported in Aegle marmelos whereas prolate in Lantana camara. Moreover, quantitative characters also aid well for species delimitation, such as prolate pollen found in both Cestrum diurnum and Terminalia chebula Retz. but both of these varied in their P/E ratio, that is, 0.97 and 0.88, respectively. The leaf epidermal characters in correlation with morph-palynological traits showed potential for taxonomic resolution at the species level. RESEARCH HIGHLIGHTS: This study provides valuable morpho-anatomical and morpho-palynological tools for the nine traditional therapeutic plants of the district, Lahore, Pakistan. Light and scanning electron microscopic studies provided useful systematic data for the identification of studied plants. This systematic data include moprho-anatomical and morpho-palynological keys for the studied plants. This data can be used for future identification purposes.
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http://dx.doi.org/10.1002/jemt.23632DOI Listing
April 2021

Frequency of Normal Birth Length and Its Determinants: A Cross-Sectional Study in Newborns.

Cureus 2020 Sep 20;12(9):e10556. Epub 2020 Sep 20.

Pathology, Liaquat National Hospital and Medical College, Karachi, PAK.

Objectives There are several factors that may affect the length and height of the infant. Maternal factors include a wide array of factors (anthropometric, hematological, or genetic), which can affect newborn health determinants. The objective of this study was to evaluate the frequency of normal birth length and its determinants in newborns. Methods This retrospective cross-sectional study was carried out at the Obstetrics and Gynaecological Department of Hamdard Hospital, Karachi, Pakistan, from March 1, 2019, to August 31, 2019. The relevant data were gathered by trained data collectors with the help of a structured questionnaire designed specifically for the study after taking written informed consent from all the participants. Data analysis was performed using Statistical Package for Social Sciences Version 20. Binary logistic regression was applied to develop a risk assessment model for the study outcome. Results Out of 195 pregnant mothers, 57 (29.2%) had low birth weight infants. Mean age of mothers was 29.29±5.22 years, 142 (72.8%) had BMI of 25.0 or more, 102 (52.3%) had hemoglobin between 10 to 11 mg/dL, 172 (88.2%) used to take vitamin C and iron during pregnancy, 136 (69.7%) consumed extra meals during pregnancy, and only 5 (2.6%) were tobacco smokers/chewers. Hundred (51.3%) newborns had normal birth length, i.e., >48 cm. The mother's mid-arm circumference > 22 cm (adjusted odds ratio [AOR]: 4.719; 95% CI: 2.337-9.527; p<0.001), consumption of extra meals during pregnancy (AOR: 3.947; 95% CI: 1.627-9.574; p=0.002), hemoglobin > 11 mg/dL (AOR: 4.314; 95% CI: 1.779-10.463; p=0.001), and adequate rest during pregnancy (AOR: 3.798; 95% CI: 1.464-9.848; p=0.006) were significantly associated with normal birth length of the infants, i.e., >48 cm. Conclusions Mother's mid-arm circumference > 22 cm, consumption of extra meals during pregnancy, hemoglobin > 11 mg/dL, and adequate rest during pregnancy were found to be significant predictors of normal birth length of the infants.
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http://dx.doi.org/10.7759/cureus.10556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575309PMC
September 2020

Restoration of PP2A levels in inflamed microglial cells: Important for neuroprotective M2 microglial viability.

Toxicol Appl Pharmacol 2020 12 16;409:115294. Epub 2020 Oct 16.

Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India. Electronic address:

PP2A, a trimeric Serine/Threonine Protein Phosphatase 2A highly expressed in brain, is a master regulator of cellular functions. Reduction in PP2A activity has been linked to progression of microglial mediated neuroinflammatory diseases. Inflammatory conditions are characterized by increased population of CD86 M1 cells and a therapeutic strategy to polarize microglial cells towards CD206 M2 cells is the need of hour. In this paper we analyzed A: whether the level of PP2A is altered in CD86 cells, B: whether FTY720, a known modulator of PP2A, is able to restore the level of PP2A in inflamed CD86 cells. Results revealed that PP2A activity was significantly diminished in inflamed cells but the surprising observation was the cell viability of only 35.99% upon FTY720 treatment in inflamed cells lacking basal PP2A activity. A sharp increase at mRNA level of CD95 and ASK-1 indicated that apoptosis occurred in these cells through CD95/ASK-1/JNK pathway. Importantly, flow cytometric analysis revealed apoptosis of not only CD86 cells but also CD206 cells. Previous studies have reported that FTY720 polarizes microglial cells towards M2 states; however apoptosis of M2 cells was not studied. As western blot analysis revealed that FTY720 failed to completely restore PP2A, another PP2A modulator, Memantine, was used for co-treatment. Upon co-treatment, the level of PP2A was completely restored and also viability of microglial cells was significantly improved with a significant reduction in apoptosis of M2 cells. These findings suggest that co-treatment strategy may prove beneficial to balance M1/M2 microglial population, thereby improving neuronal functions.
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http://dx.doi.org/10.1016/j.taap.2020.115294DOI Listing
December 2020

Design and synthesis of pyrazole-pyrazoline hybrids as cancer-associated selective COX-2 inhibitors.

Arch Pharm (Weinheim) 2021 Jan 4;354(1):e2000116. Epub 2020 Oct 4.

Drug Design and Medicinal Chemistry Laboratory, Jamia Hamdard, New Delhi, India.

In continuation of our previous work on cancer and inflammation, 15 novel pyrazole-pyrazoline hybrids (WSPP1-15) were synthesized and fully characterized. The formation of the pyrazoline ring was confirmed by the appearance of three doublets of doublets in H nuclear magnetic resonance spectra exhibiting an AMX pattern for three protons (H , H , and H ) of the pyrazoline ring. All the synthesized compounds were screened for their in vitro anticancer activity against five cell lines, that is, MCF-7, A549, SiHa, COLO205, and HepG2 cells, using the MTT growth inhibition assay. 5-Fluorouracil was taken as the positive control in the study. It was observed that, among them, WSPP11 was found to be active against A549, SiHa, COLO205, and HepG2 cells, with IC values of 4.94, 4.54, 4.86, and 2.09 µM. All the derivatives were also evaluated for their cytotoxicity against HaCaT cells. WSPP11 was also found to be nontoxic against normal cells (cell line HaCaT), with an IC value of more than 50 µM. The derivatives were also evaluated for their in vitro anti-inflammatory activity by the protein (egg albumin) denaturation assay and the red blood cell membrane stabilizing assay, using diclofenac sodium and celecoxib as standard. Compounds that showed significant anticancer and anti-inflammatory activities were further studied for COX-2 inhibition. The manifestation of a higher COX-2 selectivity index of WSPP11 as compared with other derivatives and an in vitro anticancer activity against four cell lines further established that compounds that were more selective toward COX-2 also exhibited a better spectrum of activity against various cancer cell lines.
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http://dx.doi.org/10.1002/ardp.202000116DOI Listing
January 2021

Synthesis, ADMET prediction and reverse screening study of 3,4,5-trimethoxy phenyl ring pendant sulfur-containing cyanopyrimidine derivatives as promising apoptosis inducing anticancer agents.

Bioorg Chem 2020 11 19;104:104282. Epub 2020 Sep 19.

Drug Design & Medicinal Chemistry Lab, Department of Pharmaceutical Chemistry, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India. Electronic address:

Cancer remains considered as one of the leading global health problems either due to meagre and suboptimal therapeutic response of chemotherapeutic agents or due to the emergence of spontaneous complex multidrug resistance in cancer cells. This created a persistent need for the development of new anticancer agents. Enthralled by the high success rate for natural product-based drug discovery and current research scenario, we synthesized a new series of 3,4,5-trimethoxy phenyl ring pendant sulfur-containingcyanopyrimidine derivatives clubbed with different amines intending to search an anticancer lead compound. To probe the anti-proliferative spectrum of the synthesized derivatives, an in-vitro evaluation was piloted against a panel of 60 cancer cell lines at the National Cancer Institute (NCI) representing major types of cancer diseases. Most of the derivatives showed good to moderate anti-proliferative activity. The results revealed that compound 4e displayed the most promising broad-spectrum anticancer activity with high growth inhibition of various cell lines representing multiple cancers diseases. Mechanistic investigation of compound 4e in human breast cancer MDA-MB-231 cells showed that compound 4e triggers cell death through the induction of apoptosis. ADMET studies and reverse screening were also performed to identify the potential targets of designed molecules. It was concluded that 3,4,5-trimethoxy phenyl ring pendant sulfur-containingcyanopyrimidine derivative 4e could act as a promising hit molecule for further development of novel anticancer therapeutics.
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http://dx.doi.org/10.1016/j.bioorg.2020.104282DOI Listing
November 2020

Gut Microbiome and Depression: How Microbes Affect the Way We Think.

Cureus 2020 Aug 23;12(8):e9966. Epub 2020 Aug 23.

Psychiatry, California Institute of Behavioral Neurosciences and Psychology, Fairfield, USA.

The gut microbiome serves an important role in the human body. Reportedly, one of the benefits of these microflora is on mental health. Once established, food and other dietary sources that enhance quality microbiome content in our gastrointestinal system will be a significant consideration in individuals' day to day lives. This literature review conducted a PubMed search for studies about the gut microbiome and its relation to depression. In using several Medical Subject Heading (MeSH) keywords, relevant literature was selected. A total of 26 articles were selected after applying the inclusion and exclusion criteria, and after checking the articles' accessibility. This literature would like to establish the role of the gut microbiome in depression. This study's findings showed that there is a strong association of microbiome function to mental well-being.
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http://dx.doi.org/10.7759/cureus.9966DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510518PMC
August 2020

Refugee and Migrant Children's Mental Healthcare: Serving the Voiceless, Invisible, and the Vulnerable Global Citizens.

Cureus 2020 Aug 22;12(8):e9944. Epub 2020 Aug 22.

Medicine, Windsor University School of Medicine, Basseterre, KNA.

Millions of children are on the run worldwide, with many unaccompanied children and adolescents undertaking risky journeys to flee war, adverse circumstances, and political persecution. The grueling journey and multiple stressors faced by the refugee children, both accompanied and unaccompanied during the pre-migration, migration, and in the country of destination, increase their risk for psychiatric disorders and other medical conditions. Unaccompanied refugee migrant children have higher prevalence of mental health disorders than accompanied refugee peers. Long after reaching the host country, the refugee, migrant, and asylum-seeking juveniles continue to face adversities in the form of acculturation. In assessing medical fitness and healthcare mediations for refugees and migrant children, special consideration should be given to certain areas such as their distinct history, whether they are with their family or separated or unaccompanied, and whether they have been peddled or have been left behind.
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http://dx.doi.org/10.7759/cureus.9944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505673PMC
August 2020

Refugee and Migrant Children's Mental Healthcare: Serving the Voiceless, Invisible, and the Vulnerable Global Citizens.

Cureus 2020 Aug 22;12(8):e9944. Epub 2020 Aug 22.

Medicine, Windsor University School of Medicine, Basseterre, KNA.

Millions of children are on the run worldwide, with many unaccompanied children and adolescents undertaking risky journeys to flee war, adverse circumstances, and political persecution. The grueling journey and multiple stressors faced by the refugee children, both accompanied and unaccompanied during the pre-migration, migration, and in the country of destination, increase their risk for psychiatric disorders and other medical conditions. Unaccompanied refugee migrant children have higher prevalence of mental health disorders than accompanied refugee peers. Long after reaching the host country, the refugee, migrant, and asylum-seeking juveniles continue to face adversities in the form of acculturation. In assessing medical fitness and healthcare mediations for refugees and migrant children, special consideration should be given to certain areas such as their distinct history, whether they are with their family or separated or unaccompanied, and whether they have been peddled or have been left behind.
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http://dx.doi.org/10.7759/cureus.9944DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7505673PMC
August 2020

Does Catheter Ablation Lower the Long-Term Risk of Stroke and Mortality in Patients with Atrial Fibrillation? A Concise Review of the Current State of Knowledge.

Cureus 2020 Aug 12;12(8):e9701. Epub 2020 Aug 12.

Internal Medicine, California Institute of Behavioural Neurosciences and Psychology, Fairfield, USA.

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide and carries a significant risk of morbidity and mortality. Multiple trials have highlighted the benefit of catheter ablation over medical therapy in restoring sinus rhythm and improving quality of life. Whether it reduces long-term risk of stroke and mortality is still unclear. We performed a literature search using the PubMed database to review the current state of knowledge regarding the long-term outcomes of stroke and mortality in ablated patients compared to patients who receive medical therapy. Our review mainly consisted of recent randomized controlled trials and large observational studies.  Results from large observational studies show that catheter ablation significantly reduces the risk of stroke in high-risk patients and mortality compared to medical therapy. However, randomized controlled trials have only demonstrated a mortality benefit in patients with comorbid systolic heart failure. In patients with paroxysmal AF, ablation therapy significantly limits the progression to persistent AF and has a higher efficacy in restoring sinus rhythm. Maintenance of sinus rhythm is the most important factor associated with lower long term risk of stroke and mortality. Large randomized controlled trials similar to the Catheter Ablation Versus Anti-arrhythmic Drug Therapy for Atrial Fibrillation (CABANA) trial are still needed to clarify whether catheter ablation is superior over medical therapy in improving the long-term outcomes of stroke and mortality.
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http://dx.doi.org/10.7759/cureus.9701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486083PMC
August 2020

Does Catheter Ablation Lower the Long-Term Risk of Stroke and Mortality in Patients with Atrial Fibrillation? A Concise Review of the Current State of Knowledge.

Cureus 2020 Aug 12;12(8):e9701. Epub 2020 Aug 12.

Internal Medicine, California Institute of Behavioural Neurosciences and Psychology, Fairfield, USA.

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide and carries a significant risk of morbidity and mortality. Multiple trials have highlighted the benefit of catheter ablation over medical therapy in restoring sinus rhythm and improving quality of life. Whether it reduces long-term risk of stroke and mortality is still unclear. We performed a literature search using the PubMed database to review the current state of knowledge regarding the long-term outcomes of stroke and mortality in ablated patients compared to patients who receive medical therapy. Our review mainly consisted of recent randomized controlled trials and large observational studies.  Results from large observational studies show that catheter ablation significantly reduces the risk of stroke in high-risk patients and mortality compared to medical therapy. However, randomized controlled trials have only demonstrated a mortality benefit in patients with comorbid systolic heart failure. In patients with paroxysmal AF, ablation therapy significantly limits the progression to persistent AF and has a higher efficacy in restoring sinus rhythm. Maintenance of sinus rhythm is the most important factor associated with lower long term risk of stroke and mortality. Large randomized controlled trials similar to the Catheter Ablation Versus Anti-arrhythmic Drug Therapy for Atrial Fibrillation (CABANA) trial are still needed to clarify whether catheter ablation is superior over medical therapy in improving the long-term outcomes of stroke and mortality.
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http://dx.doi.org/10.7759/cureus.9701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7486083PMC
August 2020

The Impact of Impulsivity and Emotional Dysregulation on Comorbid Bipolar Disorder and Borderline Personality Disorder.

Cureus 2020 Aug 5;12(8):e9581. Epub 2020 Aug 5.

Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA.

The symptomatic overlap between borderline personality disorder (BPD) and bipolar disorder (BD) is a topic of scientific and academic debates. Emotional dysregulation and impulsivity are common features of both disorders. Several studies have shown that both BPD and BD lie on a spectrum; others have suggested that they are separate entities that coexist.  BPD is characterized by impulsive and dangerous behaviors such as driving recklessly, inappropriate sexual behavior, eating disorders, and substance abuse. BD, during a manic episode, is known for their impulsive and risk-taking behavior like hypersexuality, excessive spending, and substance abuse.  The current literature review aims to provide an overview of the impact of impulsivity and emotional dysregulation on comorbid bipolar disorder and borderline personality disorder. Our study results showed that patients with comorbid BPD and BD struggle with impulsive actions and have difficulty controlling their emotions. They are also highly susceptible to anxiety disorders like obsessive-compulsive disorder (OCD), post-traumatic stress disorder (PTSD), and somatoform disorders. Patients with comorbid BPD and BD struggle with severe psychosocial morbidity and an increased risk of suicide. In patients with only one disease, misdiagnosis is a common phenomenon due to the overlapping symptoms of BPD and BD.
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http://dx.doi.org/10.7759/cureus.9581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7478747PMC
August 2020

Light microscopy and scanning electron microscopy of bacterial colonies isolated from ras malai samples from different markets of Lahore, Pakistan.

Microsc Res Tech 2020 Nov 7;83(11):1417-1426. Epub 2020 Sep 7.

Department of Plant Sciences, Lahore College for Women University, Lahore, Pakistan.

The current study investigates the total bacterial contamination in various packed and unpacked ras malai samples of 14 different localities of Lahore, Pakistan. The bacterial colonies such as Bacillus sp. and Gamella sp. were isolated from ras malai samples and grown on agar-broth media under sterile environmental conditions. Serial dilution technique was used to compose the replicates to get a viable count of bacteria in the samples. Results indicated that in case of packed ras malai samples, maximum bacterial count was observed in Sample 1 (422 × 10 to 402 × 10 ) and minimum bacterial count was in Sample 4 (21 × 10 to 9.3 × 10 ). For unpacked ras malai samples, maximum bacterial count was in Sample 3 (200.3 × 10 to 181.3 × 10 ) and minimum bacterial count was observed in Sample 1 (110 × 10 to 90.4 × 10 ). It was concluded that the marketed samples contain more bacterial count as compared to the standard sterilization values. Such products could possibly become the cause of many health problems in children.
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http://dx.doi.org/10.1002/jemt.23534DOI Listing
November 2020

Light and scanning electron microscopic characterization of thirty endemic Fabaceae species of district Lahore, Pakistan.

Microsc Res Tech 2020 Dec 1;83(12):1507-1529. Epub 2020 Sep 1.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

In the present study anatomical characterization of 30 species of Fabaceae endemic to Lahore, Pakistan were done under light and scanning electron microscopy. Variety of qualitative and quantitative anatomical characters like epidermal cells shapes and size, stomata types, length, and width of guard cells, subsidiary cells, trichomes, silica bodies, shapes, and their numbers were studied. Overall polygonal, irregular smooth, thick walled epidermal cells were observed at both abaxial and adaxial surfaces except Dalbergia sisso Roxb in which hexagonal epidermal cells were reported. Milletia ovelifolia Kurz. possessed the largest length of epidermal cell i.e., 273.1 μm whereas Calliandra bella Benth. showed the smallest length i.e., 76.5 μm. Average width of epidermal cells ranged from 44 to 265.5 μm. M. ovelifolia Kurz had largest width while Acacia nilotica L. had the smallest width respectively. In adaxial surface epidermal cells length ranged 317 to 46.4 μm, Glycyrriza glabra L. showed the smallest length whereas Prosopis juliflora DC. had largest length. In adaxial numbers of stomata is high as compare to the abaxial surface, mostly paracytic, anisocytic, and anomocytic stomata were observed. There is not much variations observed in trichomes of studied members. Generally non glandular, unbranched, uniserate, mulicellular bulbous base with pointed tips were reported . Oval, rounded, triangular shaped silica bodies were observed in some species. It is concluded that qualitative and quantitative anatomical variations in epidermal cells, stomata and trichomes are of good taxonomic value for the studied Fabaceae species.
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http://dx.doi.org/10.1002/jemt.23545DOI Listing
December 2020

Traits, Trends, and Trajectory of Tween and Teen Cyberbullies.

Cureus 2020 Aug 14;12(8):e9738. Epub 2020 Aug 14.

Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA.

Digital communication has revolutionized the way children interact and maintain social relations. However, not every tween (8-12 years) or teen (13-18 years) is able to take full advantage of digital media and may cross personal and social boundaries causing distress, mostly to their own friends at school and beyond. This results in adverse health effects for both the cyberbullying perpetrator and the victim. Articles reviewed on elementary school children and adolescents, collected from two different databases, showed that the number of elementary school kids using smartphones has more than doubled in the past few years. Given this rise, the risk of cyberbullying has also increased. Not all elementary school kids have the required media literacy to understand that their friends have equal rights in the virtual world as they do in the schoolyard. Regardless, they still carry a smartphone with data, use computers, and other electronic media to bully, embarrass, exclude, or humiliate others, often through social networking sites. Moving from tweens to teens seems to worsen the cyberbully behavior and choices, with middle school kids facing the highest cyberbullying incidents followed by high school kids and then the elementary school kids. The anonymity of cyberspace and the perceived lack of consequences seems to embolden the cyberbully. Identifying the mindset of a cyberbully and those at high risk of becoming a cyberbully can help target intervention efforts where they are needed the most and prevent cyberbullying.
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http://dx.doi.org/10.7759/cureus.9738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7430539PMC
August 2020

Frequency of Low Birth Weight and its Relationship With Maternal Nutritional and Dietary Factors: A Cross-Sectional Study.

Cureus 2020 Jun 21;12(6):e8731. Epub 2020 Jun 21.

Internal Medicine, Dow University of Health Sciences, Karachi, PAK.

Background:  Low birth weight (LBW) is linked with fetal and neonatal mortality and morbidity; also it can slow down growth and cognitive development. Several factors contribute to pregnancy outcomes, including LBW deliveries, maternal nutrition, and additional dietary intake. Our study was aimed to identify the frequency and factors associated with LBW mothers in Karachi, Pakistan.  Methods: A cross-sectional survey was carried out at the Obstetrics and Gynaecological Department of Hamdard Hospital, Karachi. A total of 195 healthy pregnant females were enrolled. All the relevant data were collected from March 1st, 2019 to August 31st, 2019 with the help of a structured questionnaire designed specifically for the study where mothers were also asked about consumption of iron, vitamin, and extra meals since they became pregnant. Written, informed consent was taken from all of the participants before data collection. Data analysis was performed using a statistical package for the social sciences (SPSS) version 20.0. A Chi-square test was used for checking associations between the studied maternal factors and the weight of the children.  Results: There was a total of 195 pregnant females selected for the study. The frequency of LBW infants was found to be 57 (29.2%) in these women. The mean age of the females was 29.29 ± 5.22 years, 142 (72.8%) of them had a body mass index (BMI) of 25.0 kg/m or more, 102 (52.3%) of them had hemoglobin (Hb) between 10 and 11 mg/dL. The study results further showed that maternal Hb (p=0.02), vitamin C intake (p=0.037), iron intake (p=0.01), and consumption of extra meals during pregnancy (p=0.021) were significantly associated with a LBW of the children. Mothers whose Hb <10 mg/dL, no intake of vitamin C, or iron, and extra meals during pregnancy were more likely to have a child with LBW than others.

Conclusion:  It can be concluded that maternal nutritional and dietary factors are very important during fetal development, and they have a significant relationship with the birth weight.
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http://dx.doi.org/10.7759/cureus.8731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7374259PMC
June 2020

Applications of scanning electron microscopy in taxonomy with special reference to family Euphorbiaceae.

Microsc Res Tech 2020 Sep 9;83(9):1066-1078. Epub 2020 Jun 9.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

The present study was carried out to identify the 20 medicinally important species of family Euphorbiaceae by the aid of scanning electron microscopy (SEM) of the foliar anatomical characteristics. Both qualitative and quantitative measurements for the anatomical characters like epidermal cells, stomata, trichomes, and subsidiary cells on both abaxial(ab) and adaxial(ad) epidermis were recorded. Remarkable variations in these anatomical features had been observed among the studied Euphorbiaceae species. Most species had epidermal cells irregular or polygonal in shape, only five species had hexagonal cells, that is, Euphorbia neriifolia L., Euphorbia prostate Aiton, Jatropha integerrima Jacq., Vernicia fordii (Hemsl.), and Euphorbia royleana Boiss. Stomata were abundant on abaxial epidermis as compared to adaxial epidermis. E. prostate Aiton, Euphorbia pulcherrima Willd. Ex Klotzsch and Phyllanthus emblica L. possessed anomocytic stomata, and Euphorbia helioscopia L., Euphorbia cotinifolia L., E. neriifolia L., and Ricinus communis L. possessed anisocytic stomata, while rest of the species had paracytic stomata. Trichomes were present in very few species including Euphorbia hirta L., E. prostate Aiton, E. pulcherrima Willd. Ex Klotzsch, and Putranjiva roxburghii Wall. Similarly, variations were also reported by quantitative features such as E. helioscopia L. can be distinguished from E. hirta on the basis of length of epidermal cells, that is, 103.4 ± 0.15 and 74.9 ± 0.55 μm, respectively. Moreover, E. pulcherrima Willd. Ex Klotzsch had trichomes with the length of 408 ± 0.55 μm and P. roxburghii Wall. had trichome with the length of 314.2 ± 1.35 μm, respectively. These findings confirmed that taxonomic utility of the anatomical traits for the identification of studied Euphorbiaceae taxa.
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http://dx.doi.org/10.1002/jemt.23497DOI Listing
September 2020

Scanning electron microscopic screening of 20 medicinally important Asteroideae taxa.

Microsc Res Tech 2020 Aug 5;83(8):988-1006. Epub 2020 May 5.

Department of Botany, Lahore College for Women University, Lahore, Pakistan.

In the present study anatomical characterization of 20 medicinally important Asteroideae species were done under light and scanning electron microscopy. Variety of qualitative and quantitative anatomical characters like epidermal cells, stomata, guard cells, subsidiary cells, trichomes and oil droplets were observed. Generally pentagonal, polygonal, irregular or hexagonal, smooth, undulating thick walled epidermal cells were observed in studied species. In abaxial surface Thymophylla tenuiloba L. possessed the largest length of epidermal cell that is, 221.6 (156.6-286.6) μm whereas Bellis perenis L. showed the smallest length that is, 46.4 (32.6-60.2) μm. Average width of epidermal cells ranged from 57 (22-92) μm to 169 (127.9-210.1) μm. Cosmos sulphureus Cav. had smallest width while Thymophylla tenuiloba L. had the largest width. In adaxial surface Artemisia absinthium L. possessed the largest length of epidermal cell that is, 269 (165.1-372.9) μm whereas Bellis perenis L. showed the smallest length that is, 61.4 (42.6-80.2) μm. Average width of epidermal cells ranged from 50.8 (32.6-69) μm to 260 (116-202) μm. Thymophylla tenuiloba L. had smallest width while Dahlia pinnata Cav. had the largest width. Among stomatal characters anisocytic, anomocytic, and diacytic stomata were observed in selected species of Asteroideae. Nonglandular uniserate, multicellular, unbranched pointed tips with bulbous base trichomes were reported in some Asteroideae members while some possessed glandular, capitates mushroom like multicellular trichomes covered with tubercle papicles. Rounded, oval, triangular shaped oil droplets were observed in some species. It is concluded that qualitative and qualitative anatomical variations in trichomes, stomata and epidermal cells are of good taxonomic value for the Asteroideae species.
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http://dx.doi.org/10.1002/jemt.23492DOI Listing
August 2020

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv.

Gigascience 2019 11;8(11)

Common Workflow Language Project.

Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable automation, scaling, adaptation, and provenance support. However, there are still several challenges associated with the effective sharing, publication, and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms.

Results: Based on best-practice recommendations identified from the literature on workflow design, sharing, and publishing, we define a hierarchical provenance framework to achieve uniformity in provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realize this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We use open source community-driven standards, interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric research objects generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups.

Conclusions: The underlying principles of the standards utilized by CWLProv enable semantically rich and executable research objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, reuse the methods for partial reruns, or reproduce the analysis to validate the published findings.
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http://dx.doi.org/10.1093/gigascience/giz095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824458PMC
November 2019
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