Publications by authors named "Atikur Rahman"

38 Publications

Determinants of children ever born among ever-married women in Bangladesh: evidence from the Demographic and Health Survey 2017-2018.

BMJ Open 2022 06 29;12(6):e055223. Epub 2022 Jun 29.

School of Sciences, University of Southern Queensland, Toowoomba, Queensland, Australia.

Objective: To investigate the prevalence of the number of children ever born (CEB) and its associated determinants among women aged 15-49 years in Bangladesh.

Study Design And Setting: We used clustered data extracted from the last two Bangladesh Demographic and Health Surveys (BDHS 2014 and BDHS 2017-2018). A two-stage stratified sampling was used in both surveys. Mixed logistic regression modelling approach for binary responses was adapted to accommodate clustering effects via the generalised linear mixed model framework.

Participants: The study is based on 15 924 ever-married women in BDHS 2017-2018 (14 119 in BDHS 2014) of Bangladesh.

Results: As per the latest BDHS 2017-2018, 42.1% of reproductive women had three or more children. Age at first marriage (p<0.001, OR 0.74, 95% CI 0.666 to 0.825), age at first birth (p<0.001, OR0.54, 95% CI 0.480 to 0.607), place of residence (p<0.001, OR 0.79, 95% CI 0.712 to 0.872), exposure of media (p<0.001, OR 0.71, 95% CI 0.647 to 0.768), religion (p<0.001, OR 1.47, 95% CI 1.277 to 1.690), husband's desire more child (p<0.001, OR 1.60, 95% CI 1.428 to 1.784), women empowerment (p<0.001, OR 1.19, 95% CI 1.075 to 1.3) and wealth index (p<0.001, OR1.61, 95% CI 0.435 to 1.796) were found to be statistically significant determinants of the number of CEB among ever-married women. The number of CEB among women was negatively associated with their own educational status (p<0.001) and husbands level of education (p<0.001).

Conclusion: The CEB appears to be higher among women who were married before 18 years, Muslim, illiterate, living in rural areas, had first birth before 20 years, non-exposure of media and husband's desire for more children.
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http://dx.doi.org/10.1136/bmjopen-2021-055223DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9244679PMC
June 2022

An assessment of random forest technique using simulation study: illustration with infant mortality in Bangladesh.

Health Inf Sci Syst 2022 Dec 21;10(1):12. Epub 2022 Jun 21.

Department of Statistics, Jahangirnagar University, Dhaka, Bangladesh.

We aimed to assess different machine learning techniques for predicting infant mortality (<1 year) in Bangladesh. The decision tree (DT), random forest (RF), support vector machine (SVM) and logistic regression (LR) approaches were evaluated through accuracy, sensitivity, specificity, precision, F1-score, receiver operating characteristics curve and -fold cross-validation via simulations. The Boruta algorithm and chi-square ( ) test were used for features selection of infant mortality. Overall, the RF technique (Boruta: accuracy = 0.8890, sensitivity = 0.0480, specificity = 0.9789, precision = 0.1960, F1-score = 0.0771, AUC = 0.6590; : accuracy = 0.8856, sensitivity = 0.0536, specificity = 0.9745, precision = 0.1837, F1-score = 0.0828, AUC = 0.6480) showed higher predictive performance for infant mortality compared to other approaches. Age at first marriage and birth, body mass index (BMI), birth interval, place of residence, religion, administrative division, parents education, occupation of mother, media-exposure, wealth index, gender of child, birth order, children ever born, toilet facility and cooking fuel were potential determinants of infant mortality in Bangladesh. Study findings may help women, stakeholders and policy-makers to take necessary steps for reducing infant mortality by creating awareness, expanding educational programs at community levels and public health interventions.
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http://dx.doi.org/10.1007/s13755-022-00180-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9209612PMC
December 2022

The impact of land use and land cover change on groundwater recharge in northwestern Bangladesh.

J Environ Manage 2022 Aug 25;315:115130. Epub 2022 Apr 25.

Department of Irrigation and Water Management, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh; Water, Energy and Environmental Engineering Research Unit, University of Oulu, P.O. Box 4300, FIN90014, Oulu, Finland; School of Geosciences, University of Aberdeen, Old Aberdeen, AB24 3UF, Scotland, UK. Electronic address:

Groundwater recharge is affected by various anthropogenic activities, land use and land cover (LULC) change among these. The long-term temporal and seasonal changes in LULC have a substantial influence on groundwater flow dynamics. Therefore, assessment of the impacts of LULC changes on recharge is necessary for the sustainable management of groundwater resources. The objective of this study is to examine the effects of LULC changes on groundwater recharge in the northwestern part of Bangladesh. Spatially distributed monthly groundwater recharge was simulated using a semi-physically based water balance model. Long-term temporal LULC change analysis was conducted using LULC maps from 2006 to 2016, while wet and dry LULC maps were used to examine seasonal changes. The results show that the impervious built-up area has increased by 80.3%, whereas vegetated land cover has decreased by 16.4% over the study period. As a result, groundwater recharge in 2016 has decreased compared to the level seen in 2006. However, the decrease in recharge due to long-term temporal LULC changes is very small at the basin scale (2.6 mm/year), although the impact on regional level is larger (17.1 mm/year) due to urbanization. Seasonal LULC variations also affect recharge due to the higher potential for dry seasonal LULC compared to the wet seasonal LULC, a substantial difference (20.6 mm/year). The results reveal important information about the groundwater system and its response to land cover changes in northwestern Bangladesh.
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http://dx.doi.org/10.1016/j.jenvman.2022.115130DOI Listing
August 2022

Prevalence and predicting factors of perceived stress among Bangladeshi university students using machine learning algorithms.

J Health Popul Nutr 2021 11 27;40(1):50. Epub 2021 Nov 27.

Bangladesh Breastfeeding Foundation (BBF), Institute of Public Health, Dhaka, Bangladesh.

Background: Stress-related mental health problems are one of the most common causes of the burden in university students worldwide. Many studies have been conducted to predict the prevalence of stress among university students, however most of these analyses were predominantly performed using the basic logistic regression (LR) model. As an alternative, we used the advanced machine learning (ML) approaches for detecting significant risk factors and to predict the prevalence of stress among Bangladeshi university students.

Methods: This prevalence study surveyed 355 students from twenty-eight different Bangladeshi universities using questions concerning anthropometric measurements, academic, lifestyles, and health-related information, which referred to the perceived stress status of the respondents (yes or no). Boruta algorithm was used in determining the significant prognostic factors of the prevalence of stress. Prediction models were built using decision tree (DT), random forest (RF), support vector machine (SVM), and LR, and their performances were evaluated using parameters of confusion matrix, receiver operating characteristics (ROC) curves, and k-fold cross-validation techniques.

Results: One-third of university students reported stress within the last 12 months. Students' pulse rate, systolic and diastolic blood pressures, sleep status, smoking status, and academic background were selected as the important features for predicting the prevalence of stress. Evaluated performance revealed that the highest performance observed from RF (accuracy = 0.8972, precision = 0.9241, sensitivity = 0.9250, specificity = 0.8148, area under the ROC curve (AUC) = 0.8715, k-fold accuracy = 0.8983) and the lowest from LR (accuracy = 0.7476, precision = 0.8354, sensitivity = 0.8250, specificity = 0.5185, AUC = 0.7822, k-fold accuracy = 07713) and SVM with polynomial kernel of degree 2 (accuracy = 0.7570, precision = 0.7975, sensitivity = 0.8630, specificity = 0.5294, AUC = 0.7717, k-fold accuracy = 0.7855). Overall, the RF model performs better and authentically predicted stress compared with other ML techniques, including individual and interaction effects of predictors.

Conclusion: The machine learning framework can be detected the significant prognostic factors and predicted this psychological problem more accurately, thereby helping the policy-makers, stakeholders, and families to understand and prevent this serious crisis by improving policy-making strategies, mental health promotion, and establishing effective university counseling services.
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http://dx.doi.org/10.1186/s41043-021-00276-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8627029PMC
November 2021

Phase evolution of all-inorganic perovskite nanowires during its growth from quantum dots.

Nanotechnology 2021 Dec 3;33(8). Epub 2021 Dec 3.

Department of Physics, Indian Institute for Science Education and Research (IISER)-Pune, Dr Homi Bhabha Road, Pune-411008, India.

All-inorganic lead-halide perovskites have emerged as an exciting material owing to their excellent optoelectronic properties and high stability over hybrid organometallic perovskites. Nanowires of these materials, in particular, have shown great promise for optoelectronic applications due to their high optical absorption coefficient and low defect state density. However, the synthesis of the most promising alpha-Cesium lead iodide (-CsPbI) nanowires is challenging as it is metastable and spontaneously converts to a non-perovskite-phase. The hot-injection method is one of the most facile, well-controlled, and commonly used approaches for synthesizing CsPbXnanostructures. But the exact mechanism of growing these nanowires in this technique is not clear. Here, we show that the hot-injection method produces photoactive phases of quantum dots (QDs) and nanowires of CsPbBrand QDs of CsPbI, but CsPbInanowires are grown in their non-perovskite-phase. Monitoring the nanowire growth during the hot-injection technique and through detailed characterization, we establish that CsPbInanowires are formed in the non-perovskite phase from the beginning rather than transforming after its growth from perovskite to a non-perovskite phase. We have discussed a possible mechanism of how non-perovskite nanowires of CsPbIgrow at the expense of photoactive perovskite QDs. Our findings will help to synthesize nanostructures of all-inorganic perovskites with desired phases, which is essential for successful technological applications.
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http://dx.doi.org/10.1088/1361-6528/ac37e2DOI Listing
December 2021

Analysis of SYK Gene as a Prognostic Biomarker and Suggested Potential Bioactive Phytochemicals as an Alternative Therapeutic Option for Colorectal Cancer: An In-Silico Pharmaco-Informatics Investigation.

J Pers Med 2021 Sep 6;11(9). Epub 2021 Sep 6.

Department of Pathology, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea.

Background: SYK gene regulates the expression of SYK kinase (Spleen tyrosine kinase), an important non-receptor protein-tyrosine kinase for immunological receptor-mediated signaling, which is also considered a tumor growth metastasis initiator. An onco-informatics analysis was adopted to evaluate the expression and prognostic value of the SYK gene in colorectal cancer (CRC), the third most fatal cancer type; of late, it may be a biomarker as another targeted site for CRC. In addition, identify the potential phytochemicals that may inhibit the overexpression of the SYK kinase protein and minimize the human CRC.

Materials & Methods: The differential expression of the SYK gene was analyzed using several transcriptomic databases, including Oncomine, UALCAN, GENT2, and GEPIA2. The server cBioPortal was used to analyze the mutations and copy number alterations, whereas GENT2, Gene Expression Profiling Interactive Analysis (GEPIA), Onco-Lnc, and PrognoScan were used to examine the survival rate. The protein-protein interaction network of SYK kinase and its co-expressed genes was conducted via Gene-MANIA. Considering the SYK kinase may be the targeted site, the selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. Molecular interactions were also observed by following the Ligplot+ version 2.2. YASARA molecular dynamics simulator was applied for the post-validation of the selected phytochemicals.

Results: Our result reveals an increased level of mRNA expression of the SYK gene in colorectal adenocarcinoma (COAD) samples compared to those in normal tissues. A significant methylation level and various genetic alterations recurrence of the SYK gene were analyzed where the fluctuation of the SYK alteration frequency was detected across different CRC studies. As a result, a lower level of SYK expression was related to higher chances of survival. This was evidenced by multiple bioinformatics platforms and web resources, which demonstrated that the SYK gene can be a potential biomarker for CRC. In this study, aromatic phytochemicals, such as kaempferol and glabridin that target the macromolecule (SYK kinase), showed higher stability than the controls, and we have estimated that these bioactive potential phytochemicals might be a useful option for CRC patients after the clinical trial.

Conclusions: Our onco-informatics investigation suggests that the SYK gene can be a potential prognostic biomarker of CRC. On the contrary, SYK kinase would be a major target, and all selected compounds were validated against the protein using in-silico drug design approaches. Here, more in vitro and in vivo analysis is required for targeting SYK protein in CRC.
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http://dx.doi.org/10.3390/jpm11090888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8470848PMC
September 2021

Prevalence and transmission of COVID-19 in community and household levels of Bangladesh: Longini and Koopman epidemic modelling approach.

Int J Clin Pract 2021 Dec 1;75(12):e14921. Epub 2021 Oct 1.

Department of Statistics, University of Dhaka, Dhaka, Bangladesh.

Aim: To estimate the prevalence of COVID-19 pandemic and its transmission rates among people in both community and household levels of Bangladesh.

Methods: We use the cross-sectional online survey data of 2080 individuals, collected from 442 households during June to September 2020 in Bangladesh. The Longini and Koopman stochastic epidemic modelling approach was adapted for analysing the data. To validate the results, a simulation study was conducted using the Markov Chain Monte Carlo (MCMC) method via the Metropolis-Hastings algorithm in the context of the Bayesian framework.

Results: Overall, the prevalence of COVID-19 pandemic was 15.1% (315 out of 2080) among people in Bangladesh. This proportion was higher in smaller households (size one: 40.0%, two: 35.7% and three: 25.9%) than larger (four: 15.8%, five: 13.3%, six: 14.1%, seven: 12.5% eight: 8.7%, nine: 14.8% and ten or eleven: 5.7%). The transmission rate of COVID-19 in community people was higher (12.0%, 95% CI: 10.0% to 13.0%) than household members (9.0%, 95% CI: 6.0% to 11.0%).

Conclusion: The susceptible individuals have a higher risk of community infection than the household and the community transmission is more responsible than the household for COVID-19 pandemic in Bangladesh.
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http://dx.doi.org/10.1111/ijcp.14921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8646588PMC
December 2021

Prognostic and clinicopathological insights of phosphodiesterase 9A gene as novel biomarker in human colorectal cancer.

BMC Cancer 2021 May 20;21(1):577. Epub 2021 May 20.

Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.

Background: PDE9A (Phosphodiesterase 9A) plays an important role in proliferation of cells, their differentiation and apoptosis via intracellular cGMP (cyclic guanosine monophosphate) signaling. The expression pattern of PDE9A is associated with diverse tumors and carcinomas. Therefore, PDE9A could be a prospective candidate as a therapeutic target in different types of carcinoma. The study presented here was designed to carry out the prognostic value as a biomarker of PDE9A in Colorectal cancer (CRC). The present study integrated several cancer databases with in-silico techniques to evaluate the cancer prognosis of CRC.

Results: The analyses suggested that the expression of PDE9A was significantly down-regulated in CRC tissues than in normal tissues. Moreover, methylation in the DNA promoter region might also manipulate PDE9A gene expression. The Kaplan-Meier curves indicated that high level of expression of PDE9A gene was associated to higher survival in OS, RFS, and DSS in CRC patients. PDE9A demonstrated the highest positive correlation for rectal cancer recurrence with a marker gene CEACAM7. Furtheremore, PDE9A shared consolidated pathways with MAPK14 to induce survival autophagy in CRC cells and showed interaction with GUCY1A2 to drive CRPC.

Conclusions: Overall, the prognostic value of PDE9A gene could be used as a potential tumor biomarker for CRC.
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http://dx.doi.org/10.1186/s12885-021-08332-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8136133PMC
May 2021

Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea.

Animals (Basel) 2021 Apr 13;11(4). Epub 2021 Apr 13.

Department of Animal Science, College of Natural Resources & Life Science, Pusan National University, Miryang 50463, Korea.

Microbiota plays a critical role in the overall growth performance and health status of dairy cows, especially during their early life. Several studies have reported that fecal microbiome of neonatal calves is shifted by various factors such as diarrhea, antibiotic treatment, or environmental changes. Despite the importance of gut microbiome, a lack of knowledge regarding the composition and functions of microbiota impedes the development of new strategies for improving growth performance and disease resistance during the neonatal calf period. In this study, we utilized next-generation sequencing to monitor the time-dependent dynamics of the gut microbiota of dairy calves before weaning (1-8 weeks of age) and further investigated the microbiome changes caused by diarrhea. Metagenomic analysis revealed that continuous changes, including increasing gut microbiome diversity, occurred from 1 to 5 weeks of age. However, the composition and diversity of the fecal microbiome did not change after 6 weeks of age. The most prominent changes in the fecal microbiome composition caused by aging at family level were a decreased abundance of and and an increased abundance of . Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis indicated that the abundance of microbial genes associated with various metabolic pathways changed with aging. All calves with diarrhea symptoms showed drastic microbiome changes and about a week later returned to the microbiome of pre-diarrheal stage regardless of age. At phylum level, abundance of Bacteroidetes was decreased ( and that of Proteobacteria increased ( = 0.07) during diarrhea. PICRUSt analysis indicated that microbial metabolism-related genes, such as starch and sucrose metabolism, sphingolipid metabolism, alanine aspartate, and glutamate metabolism were significantly altered in diarrheal calves. Together, these results highlight the important implications of gut microbiota in gut metabolism and health status of neonatal dairy calves.
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http://dx.doi.org/10.3390/ani11041113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8070554PMC
April 2021

Factors associated with coverage of vitamin a supplementation among Bangladeshi children: mixed modelling approach.

BMC Public Health 2021 04 2;21(1):648. Epub 2021 Apr 2.

School of Computing and Mathematics, Charles Sturt University, Wagga Wagga, Australia.

Background: Vitamin A deficiency (VAD) is a prominent and widespread public health problem in developing countries, including Bangladesh. About 2% of all deaths among under-five children are attributable to VAD. Evidence-based information is required to understand the influential factors to increase vitamin A supplementation (VAS) coverage and reduce VAD. We investigated the potential factors affecting VAS coverage and its significant predictors among Bangladeshi children aged 6 to 59 months using the VAS clustered data extracted from the latest Bangladesh Demographic and Health Survey 2014.

Methods: Data were analysed using mixed logistic regression (MLR) modelling approach in the generalised linear mixed model framework. The MLR model performs better than logistic regression for analysing the clustered data because of its minimum Akaike information criterion value. The likelihood ratio test showed that the variance component was significant. Therefore, the clustering effect among children was inevitable to use.

Results: VAS coverage among under-five children was 63.6%, which is not optimal and below the WHO's recommendation and the country's target of 90%. Children aged 25 to 36 months (AOR = 2.07, 95% CI: 1.711 to 2.513), who had higher educated mothers (AOR = 1.37, p = 0.033, 95% CI: 1.026-1.820) and fathers (AOR = 1.32, p = 0.027, 95% CI: 1.032-1.683), whose mothers had media exposure (AOR = 1.22, p = 0.006, 95% CI: 1.059-1.408) and NGO membership (AOR = 1.24, p = 0.002, 95% CI: 1.089-1.422) were more likely to consume VAS.

Conclusion: The relevant authorities should create proactive awareness programs for highly vulnerable local communities, specifically targeted to educate the children's mothers about the necessity and benefits of childhood nutrition.
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http://dx.doi.org/10.1186/s12889-021-10735-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8017789PMC
April 2021

Molecular Characterization and Phylogenetic Analysis of MADS-Box Gene Associated with Stenospermocarpic Seedlessness in Muscadine Grapes.

Genes (Basel) 2021 02 5;12(2). Epub 2021 Feb 5.

Center for Viticulture & Small Fruit Research, Florida A&M University, Tallahassee, FL 32317, USA.

Reduced expression of MADS-box gene () is responsible for stenospermocarpic seedlessness in bunch grapes. This study is aimed to characterize the orthologous gene () in native muscadine grapes () at the molecular level and analyze its divergence from other plants. The transcripts were found in all muscadine cultivars tested and highly expressed in berries while barely detectable in leaves. RT-PCR and sequencing of predicted ORFs from diverse grape species showed that transcripts were conservatively spliced. The encoded VroAGL11 protein contains highly conserved MADS-MEF2-like domain, MADS domain, K box, putative phosphorylation site and two sumoylation motifs. The muscadine VroAGL11 proteins are almost identical (99%) to that of seeded bunch cultivar, Chardonnay, except in one amino acid (A79G), but differs from mutant protein of seedless bunch grape, Sultanina, in two amino acids, R197L and T210A. Phylogenetic analysis showed that gene of muscadine and other species formed a separate clade than that of other eudicots and monocots. Muscadine grape cultivar "Jane Bell" containing the highest percentage of seed content in berry (7.2% of berry weight) had the highest expression, but almost none to nominal expression in seedless cultivars Fry Seedless (muscadine) and Reliance Seedless (bunch). These findings suggest that gene controls the seed morphogenesis in muscadine grapes like in bunch grape and can be manipulated to induce stenospermocarpic seedlessness using gene editing technology.
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http://dx.doi.org/10.3390/genes12020232DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7915462PMC
February 2021

Influence of molybdenum and technetium doping on visible light absorption, optical and electronic properties of lead-free perovskite CsSnBr for optoelectronic applications.

RSC Adv 2021 Jan 12;11(4):2405-2414. Epub 2021 Jan 12.

Department of Physics, Pabna University of Science and Technology Pabna 6600 Bangladesh

Lead-free metal halide perovskites have nowadays become familiar owing to their potential use in solar cells and other optoelectronic applications. In this study, we carried out the structural, elastic, electronic, and optical properties of pure and metal (Mo/Tc) doped CsSnBr by using the density functional theory. The metal doping CsSnBr displays a narrowing band gap and as a result the optical functions exhibit high absorption and high conductivity in the visible region. Metal doping samples also reveal a high dielectric constant which indicates a low charge-carrier recombination rate and hence enhances the device performance. The optical absorption spectra of metal doped samples greatly shifted (red-shift) towards the lower energy region compared with the pure sample which creates a high-intensity peak in the visible region. The mechanical parameter reveals a highly ductile, soft, and flexible nature which indicates the suitability for use in thin films. The electronic band structure of metal-doped CsSnBr shows an intermediate state that assists the excited electron to pass on from valence band to conduction band. The overall study suggests that lead-free CsSnTcBr perovskite is a promising candidate for solar cells and other optoelectronic applications.
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http://dx.doi.org/10.1039/d0ra09853aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8693675PMC
January 2021

Common and Differential Dynamics of the Function of Peripheral Blood Mononuclear Cells between Holstein and Jersey Cows in Heat-Stress Environment.

Animals (Basel) 2020 Dec 24;11(1). Epub 2020 Dec 24.

Department of Animal Science, College of Natural Resources & Life Science, Pusan National University, Miryang 50463, Korea.

Heat stress has been reported to affect the immunity of dairy cows. However, the mechanisms through which this occurs are not fully understood. Two breeds of dairy cow, Holstein and Jersey, have distinct characteristics, including productivity, heat resistance, and disease in high-temperature environments. The objective of this study is to understand the dynamics of the immune response of two breeds of dairy cow to environmental change. Ribonucleic acid sequencing (RNA-seq) results were analyzed to characterize the gene expression change of peripheral blood mononuclear cells (PBMCs) in Holstein and Jersey cows between moderate temperature-humidity index (THI) and high THI environmental conditions. Many of the differentially expressed genes (DEGs) identified are associated with critical immunological functions, particularly phagocytosis, chemokines, and cytokine response. Among the DEGs, and were the top down-regulated genes in both breeds of dairy cow, and many DEGs were related to antimicrobial immunity. Functional analysis revealed that cytokine and chemokine response-associated pathways in both Holstein and Jersey PBMCs were the most important pathways affected by the THI environmental condition. However, there were also breed-specific genes and pathways that altered according to THI environmental condition. Collectively, there were both common and breed-specific altered genes and pathways in Holstein and Jersey cows. The findings of this study expand our understanding of the dynamics of immunity in different breeds of dairy cow between moderate THI and high THI environmental conditions.
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http://dx.doi.org/10.3390/ani11010019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7824059PMC
December 2020

Fine-Tuning Plasmon-Molecule Interactions in Gold-BODIPY Nanocomposites: The Role of Chemical Structure and Noncovalent Interactions.

Chempluschem 2021 01 15;86(1):87-94. Epub 2020 Oct 15.

Institute of Nano Science and Technology, Habitat Centre, Phase 10, Sector 64, Mohali, 160062, India.

Strong coupling between localized surface plasmons and molecular absorptions leads to remarkable changes in the photophysical properties of dye-loaded metal nanoparticles. Here, we report supramolecular nanocomposites consisting of BODIPY, tryptophan, and gold nanoparticles, and investigate the effect of structural variations on their photophysical properties. Our results indicate that the photostability and photosensitization properties of the nanocomposites depend on the chemical composition of the BODIPY molecules. The singlet oxygen quantum yield of the nanocomposites NC1 (BODIPY, B1 bearing a single methyl group) and NC3 (BODIPY, B3 with 5 methyl and 2 iodo groups) were 0.46 and 0.42, respectively, which were significantly higher compared to their individual components. Ultrafast spectroscopy studies revealed that the migration of photoexcited BODIPY electrons to the plasmonic photoexcitation allowed electron transfer into the singlet oxygen states, thereby leading to efficient generation of singlet oxygen.
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http://dx.doi.org/10.1002/cplu.202000545DOI Listing
January 2021

Modulating flow near substrate surface to grow clean and large-area monolayer MoS.

Nanotechnology 2020 Oct 22;31(41):415706. Epub 2020 Jun 22.

Department of Physics, Indian Institute for Science Education and Research (IISER)-Pune, Dr. Homi Bhabha Road, Pune 411008, India.

Chemical vapour deposition (CVD) is one of the most promising methods to synthesize monolayers of 2D materials like transition metal dichalcogenides (TMDs) over a large area with high film quality. Among many parameters that determine the growth of 2D materials, flow of precursor near the surface is one of the most sensitive conditions. In this study, we show how subtle changes in the flow near the substrate surface can affect the quality and coverage of the MoS monolayer. We fine tune the flow of the carrier gas near the substrate under two extreme conditions to grow large area and clean monolayer. In the first study, we grew several centimetres long continuous monolayer under the condition, which generally produces monolayers of few tens of micrometres in size without tuning the flow on the substrate surface. In the second case, we got monolayer MoS under the conditions meant for the formation of bulk MoS.We achieved this by placing blockades on the substrate surface which helped in modifying the flow near them. Through simulation, we showed how the flow is affected near these blockades and used it as a guiding rule to grow patterned continuous MoS monolayers. Detailed electrical and optical measurements were done to determine the quality of the as-grown samples. Our studies provide a way to obtain clean, large area monolayer of desired pattern by tuning the flow of precursor on the vicinity of the substrate surface even when the growth conditions in CVD are far from optimum.
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http://dx.doi.org/10.1088/1361-6528/ab9ed6DOI Listing
October 2020

Understanding the thermal degradation mechanism of perovskite solar cells via dielectric and noise measurements.

Nanotechnology 2020 Sep 29;31(36):365403. Epub 2020 May 29.

Department of Physics and Centre for Energy Science, Indian Institute of Science Education and Research (IISER)-Pune, Pune, Maharashtra 411008 India.

Long term stability is a major obstacle to the success of perovskite solar cell (PSC) photovoltaic technology. PSC performance deteriorates significantly in the presence of humidity, oxygen and exposure to UV light and heat. Here the change in charge transport properties of PSC with temperature and the associated significant drop in device performance at high temperature have been investigated. The latter is shown to be primarily due to an increase in charge carrier recombination, which impacts the open-circuit voltage. To understand the pathway of temperature-induced degradation, low-frequency 1/f noise characteristics, and the capacitance-frequency, as well as capacitance-voltage characteristics have been investigated under various conditions. The results show that at high operating temperature accumulation of ions and charge carriers at the interface increase the surface recombination. Aging experiments at different temperatures show high stability of PSCs up to temperature <70 °C, but a drastic, irreversible degradation occurs at higher temperature (≥80 °C). Low-frequency 1/f noise study revealed that the magnitude of normalized noise in degraded perovskite solar cells is four orders of magnitude higher than the pristine device. This study shows the power of low-frequency noise measurement technique as a highly sensitive non-invasive tool to study the degradation mechanism of PSCs.
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http://dx.doi.org/10.1088/1361-6528/ab97d4DOI Listing
September 2020

Primary sellar neuroblastoma mimicking invasive pituitary adenoma: a systematic review.

J Neurosurg Sci 2020 Aug 29;64(4):377-382. Epub 2020 Apr 29.

Department of Neurosurgery, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh.

Introduction: To report an extremely rare case of sellar neuroblastoma, which mimicked invasive pituitary adenoma with supra- and parasellar extensions, treated through endoscopic endonasal approach. A systematic review of the literature on diagnosis and management of patients affected by sellar neuroblastomas has been performed.

Evidence Acquiition: A literature search according to the PRISMA statement was conducted using MEDLINE, Google Scholar, and EBSCO databases, searching for the following MeSH terms: (sellar OR parasellar OR suprasellar OR sphenoidal) AND (neuroblastoma OR extranasal esthesioneuroblastoma OR central neuroblastoma).

Evidence Synthesis: Sixty-eight studies were identified. We included 16 papers in our systematic review, comprising a total of 16 patients, 37.5% males and 62.5% females, with a mean age of 47.2 years. Visual disturbances were found in 56.2% of them, hyperprolactinemia in 43.7%, panhypopituitarism in 12.5%, normal pituitary function in 6.25%, SIADH in 25%, but no data is available in 25% of cases. Brain computed tomography and magnetic resonance imaging showed suprasellar and parasellar extension in 31.2% of patients, isolated suprasellar extension in 50%, isolated parasellar extension only in 6.25%, while in 1 case involvement of the petrous apex was described. Transcranial surgery (TCS) was performed for the removal in 31.2% of patients, transsphenoidal surgery (TSS) in 43.7%, a combined approach in 12.5%, and in two cases surgery was not performed due to poor general patient conditions. Adjuvant treatment with conventional radiotherapy (CRT) was performed in 62.5% of cases, gamma knife surgery (GKS) in 18.7%; in 12.5% it was not carried out, while in one case there was no data available. Absence of recurrence was documented in 50% of patients, recurrence that required further treatments in 25%, while in 25% there was no data available.

Conclusions: Primary sellar neuroblastoma is an extremely rare entity with high propensity to recur; whole body scintigraphy is recommended to search for extracranial locations, for optimum management of the disease. Special attention should be paid to endocrinological evaluation and management.
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http://dx.doi.org/10.23736/S0390-5616.20.04931-0DOI Listing
August 2020

Quantification of In Planta Progression Through Different Infection Phases and Related Association with Components of Aggressiveness.

Phytopathology 2020 Jun 22;110(6):1208-1215. Epub 2020 Apr 22.

Crop Science Department, Teagasc, Oakpark, Carlow, R93 XE12, Ireland.

In planta growth of , causal agent of Septoria tritici blotch of wheat, during the infection process has remained an understudied topic due to the long symptomless latent period before the emergence of fruiting bodies. In this study, we attempted to understand the relationship between in planta growth of relative to the primary components of aggressiveness, i.e., latent period and pycnidia coverage in regard to contrasting host resistance. We tested isolates collected from Ireland against the susceptible cultivar Gallant and cultivar Stigg, which has strong partial resistance. A clear isolate-host interaction effect ( = 3.018; = 0.005, and = 6.008; < 0.001) for latent period and pycnidia coverage, respectively, was identified. Furthermore, during the early infection phase of latency from 5 to 11 days postinoculation (dpi), in planta growth rate of fungal biomass was significantly ( = 30.06; < 0.001) more affected by host resistance than isolate specificity ( = 1.27; = 0.27), indicating the importance of host resistance in the early infection phase. In planta growth rates in cultivar Gallant spiked between 11 and 16 dpi followed by a continuous fall onward, whereas in cultivar Stigg it was slowly progressive in nature. From correlation and regression analysis, we found that the in planta growth rate preceding the average latent period of cultivar Gallant has more influence on latency duration and pycnidia production. Likewise, correlation between component of aggressiveness and in planta growth rate of pathogen supports our understanding of aggressiveness to be driven by the pathogen's multiplication capacity within host tissue.
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http://dx.doi.org/10.1094/PHYTO-09-19-0339-RDOI Listing
June 2020

Extraction Methods Affect the Structure of Goji () Polysaccharides.

Molecules 2020 Feb 19;25(4). Epub 2020 Feb 19.

Department of Food Science and Nutrition, Zhejiang Key Laboratory for Agro-Food Processing, Fuli Institute of Food Science, Zhejiang R & D Center for Food Technology and Equipment, Zhejiang University, Hangzhou 310058, China.

Polysaccharides are considered to be the most important active substances in Goji. However, the structure of polysaccharides varies according to the extraction methods applied, and the solution used to prepare Goji polysaccharides (LBPs) were limited. Thus, it is important to clarify the connection between extraction methods and structure of Goji polysaccharide. In view of the complex composition of cell wall polysaccharides and the various forms of interaction, different extraction methods will release different parts of the cell wall. The present study compared the effects of different extraction methods, which have been used to prepare different types of plant cell wall polysaccharides based on various sources, on the structure of cell-wall polysaccharides from Goji, by the single separate use of hot water, hydrochloric acid (0.4%) and sodium hydroxide (0.6%), at both high and low temperatures. Meanwhile, in order to explore the limitations of single extraction, sequential extraction methods were applied. Structural analysis including monosaccharide analysis, GPC-MALLS, AFM and H-NMR suggested the persistence of more extensively branched rhamnogalacturonan I (RG-I) domains in the procedures involving low-temperature-alkali, while procedures prepared by high-temperature-acid contains more homogalacturonan (HG) regions and results in the removal of a substantial part of the side chain, specifically the arabinan. A kind of acidic heteropolysaccharide was obtained by hot water extraction. SEC-MALLS and AFM confirmed large-size polymers with branched morphologies in alkali-extracted polysaccharides. Our results provide new insight into the extraction of Goji polysaccharides, which differ from the hot water extraction used by traditional Chinese medicine.
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http://dx.doi.org/10.3390/molecules25040936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070559PMC
February 2020

Comparative Physiological and Metabolic Analysis Reveals a Complex Mechanism Involved in Drought Tolerance in Chickpea (Cicer arietinum L.) Induced by PGPR and PGRs.

Sci Rep 2019 02 14;9(1):2097. Epub 2019 Feb 14.

Department of Agronomy, IFAS, University of Florida, Gainesville, FL, USA.

The plant growth promoting rhizobacteria (PGPR) and plant growth regulators (PGRs) can be applied to improve the growth and productivity of plants, with potential to be used for genetic improvement of drought tolerance. However, for genetic improvement to be achieved, a solid understanding of the physiological and biochemical changes in plants induced by PGPR and PGR is required. The present study was carried out to investigate the role of PGPR and PGRs on the physiology and biochemical changes in chickpea grown under drought stress conditions and their association with drought tolerance. The PGPR, isolated from the rhizosphere of chickpea, were characterized on the basis of colony morphology and biochemical characters. They were also screened for the production of indole-3-acetic acid (IAA), hydrogen cyanide (HCN), ammonia (NH), and exopolysaccharides (EPS) production. The isolated PGPR strains, named P1, P2, and P3, were identified by 16S-rRNA gene sequencing as Bacillus subtilis, Bacillus thuringiensis, and Bacillus megaterium, respectively. The seeds of two chickpea varieties, Punjab Noor-2009 (drought sensitive) and 93127 (drought tolerant) were soaked for 2-3 h prior to sowing in 24 h old cultures of isolates. The salicylic acid (SA) and putrescine (Put) were sprayed (150 mg/L) on 25 day old chickpea seedlings. The results showed that chickpea plants treated with a consortium of PGPR and PGRs significantly enhanced the chlorophyll, protein, and sugar contents compared to irrigated and drought conditions. Leaf proline content, lipid peroxidation, and activities of antioxidant enzymes (CAT, APOX, POD, and SOD) all increased in response to drought stress but decreased due to the PGPR and PGRs treatment. An ultrahigh performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) analysis was carried out for metabolic profiling of chickpea leaves planted under controlled (well-irrigated), drought, and consortium (drought plus PGPR and PGRs) conditions. Proline, L-arginine, L-histidine, L-isoleucine, and tryptophan were accumulated in the leaves of chickpea exposed to drought stress. Consortium of PGPR and PGRs induced significant accumulation of riboflavin, L-asparagine, aspartate, glycerol, nicotinamide, and 3-hydroxy-3-methyglutarate in the leaves of chickpea. The drought sensitive chickpea variety showed significant accumulation of nicotinamide and 4-hydroxy-methylglycine in PGPR and PGR treated plants at both time points (44 and 60 days) as compared to non-inoculated drought plants. Additionally, arginine accumulation was also enhanced in the leaves of the sensitive variety under drought conditions. Metabolic changes as a result of drought and consortium conditions highlighted pools of metabolites that affect the metabolic and physiological adjustments in chickpea that reduce drought impacts.
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http://dx.doi.org/10.1038/s41598-019-38702-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376124PMC
February 2019

Anomalous effect of UV light on the humidity dependence of photocurrent in perovskite solar cells.

Nanotechnology 2018 Oct 12;29(40):405701. Epub 2018 Jul 12.

Effect of oxygen on the humidity dependence of photocurrent in the presence of UV light has been studied for perovskite solar cells. We observed that the magnitude of photocurrent increases with decreasing humidity initially, but below a certain level, the photocurrent starts to decrease when the humidity is reduced by sending dry nitrogen gas. If we decrease the humidity by sending dry air (keeping nitrogen to oxygen ratio same), then this effect is absent. This phenomenon is related to the presence of oxygen in the environment. When humidity is decreased by flowing dry nitrogen, the oxygen present in the environment of perovskite solar cell also reduces. We found that in the reduced oxygen condition, the presence of UV light helps to remove oxygen from the surface of the mesoporous TiO which is responsible for the reduction of photocurrent. In the presence of white light, this effect is not observed. To understand the phenomenon we studied low-frequency noise and current-voltage characteristics, and the dielectric properties of perovskite solar cells under various conditions.
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http://dx.doi.org/10.1088/1361-6528/aad2ecDOI Listing
October 2018

Pretreatment of Wheat Bran for Suitable Reinforcement in Biocomposites.

J Renew Mater 2017 Jan;5(Suppl 1):62-73

Division of Science and Mathematics, Mayville State University, Mayville, ND 58257, USA.

Wheat bran, abundant but underutilized, was investigated for its potential as a reinforcement in biocomposites through different pretreatment methods. Pretreatment methods included were dilute sodium hydroxide (NaOH), dilute sulfuric acid (HSO), liquid hot water (LHW), calcium hydroxide (CaOH), organosolv such as aqueous ethanol (EtOH), and methyl isobutyl ketone (MIBK). Changes in chemical composition and fiber characteristics of the treated bran were studied using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). Cellulose content increased to 35.1% and 29.6% in brans treated with HSO and NaOH, respectively. The SEM micrographs showed surface cleaning of treated bran while maintaining sufficient surface roughness for the HSO, NaOH, and MIBK treated brans. Crystallinity index increased slightly for all treatments except HSO. NaOH and HSO pretreated brans achieved important fiber characteristics, which could be useful for making thermoplastic biocomposites. Innovative use of bran in thermoplastic will create more opportunities for growers while enhancing biodegradability.
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http://dx.doi.org/10.7569/JRM.2017.634133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798629PMC
January 2017

Evaluation of microbial fuel cell (MFC) for bioelectricity generation and pollutants removal from sugar beet processing wastewater (SBPW).

Water Sci Technol 2018 Jan;77(1-2):387-397

Department of Agricultural and Biosystems Engineering, North Dakota State University, Fargo, ND 58108, USA E-mail:

Bioelectricity generation from biodegradable compounds using microbial fuel cells (MFCs) offers an opportunity for simultaneous wastewater treatment. This study evaluated the synergy of electricity generation by the MFC while reducing pollutants from sugar beet processing wastewater (SBPW). A simple dual-chamber MFC was constructed with inexpensive materials without using catalysts. Raw SBPW was diluted to several concentrations (chemical oxygen demand (COD) of 505 to 5,750 mg L) and fed as batch-mode into the MFC without further modification. A power density of 14.9 mW m as power output was observed at a COD concentration of 2,565 mg L. Coulombic efficiency varied from 6.21% to 0.73%, indicating diffusion of oxygen through the cation exchange membrane and other methanogenesis and fermentation processes occurring in the anode chamber. In this study, >97% of the COD and up to 100% of the total suspended solids removals were observed from MFC-treated SBPW. Scanning electron microscopy of anode indicated that a diverse community of microbial consortia was active for electricity generation and wastewater treatment. This study demonstrated that SBPW can be used as a substrate in the MFC to generate electricity as well as to treat for pollutant removal.
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http://dx.doi.org/10.2166/wst.2017.549DOI Listing
January 2018

Patterning Superconductivity in a Topological Insulator.

ACS Nano 2017 06 31;11(6):5873-5878. Epub 2017 May 31.

Department of Physics and Astronomy, Johns Hopkins University , Baltimore, Maryland 21218, United States.

Topologically protected states in combination with superconductivity hold great promise for quantum computing applications, but the progress on electrical transport measurements in such systems has been impeded by the difficulty of fabricating devices with reliable electrical contacts. We find that superconductivity can be patterned directly into BiSe nanostructures by local doping with palladium. Superconducting regions are defined by depositing palladium on top of the nanostructures using electron beam lithography followed by in situ annealing. Electrical transport measurements at low temperatures show either partial or full superconducting transition, depending on the doping conditions. Structural characterization techniques indicate that palladium remains localized in the targeted areas, making it possible to pattern superconducting circuits of arbitrary shapes in this topological material.
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http://dx.doi.org/10.1021/acsnano.7b01549DOI Listing
June 2017

Antifogging abilities of model nanotextures.

Nat Mater 2017 06 27;16(6):658-663. Epub 2017 Feb 27.

Physique et Mécanique des Milieux Hétérogènes, UMR 7636 CNRS, ESPCI Paris, University Pierre and Marie Curie, University Denis Diderot, 75005 Paris, France.

Nanometre-scale features with special shapes impart a broad spectrum of unique properties to the surface of insects. These properties are essential for the animal's survival, and include the low light reflectance of moth eyes, the oil repellency of springtail carapaces and the ultra-adhesive nature of palmtree bugs. Antireflective mosquito eyes and cicada wings are also known to exhibit some antifogging and self-cleaning properties. In all cases, the combination of small feature size and optimal shape provides exceptional surface properties. In this work, we investigate the underlying antifogging mechanism in model materials designed to mimic natural systems, and explain the importance of the texture's feature size and shape. While exposure to fog strongly compromises the water-repellency of hydrophobic structures, this failure can be minimized by scaling the texture down to nanosize. This undesired effect even becomes non-measurable if the hydrophobic surface consists of nanocones, which generate antifogging efficiency close to unity and water departure of droplets smaller than 2 μm.
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http://dx.doi.org/10.1038/nmat4868DOI Listing
June 2017

Non-native three-dimensional block copolymer morphologies.

Nat Commun 2016 12 22;7:13988. Epub 2016 Dec 22.

Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA.

Self-assembly is a powerful paradigm, wherein molecules spontaneously form ordered phases exhibiting well-defined nanoscale periodicity and shapes. However, the inherent energy-minimization aspect of self-assembly yields a very limited set of morphologies, such as lamellae or hexagonally packed cylinders. Here, we show how soft self-assembling materials-block copolymer thin films-can be manipulated to form a diverse library of previously unreported morphologies. In this iterative assembly process, each polymer layer acts as both a structural component of the final morphology and a template for directing the order of subsequent layers. Specifically, block copolymer films are immobilized on surfaces, and template successive layers through subtle surface topography. This strategy generates an enormous variety of three-dimensional morphologies that are absent in the native block copolymer phase diagram.
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http://dx.doi.org/10.1038/ncomms13988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5196037PMC
December 2016

Effects of Extraction and Purification Methods on Degradation Kinetics and Stability of Lycopene from Watermelon under Storage Conditions.

J Food Sci 2016 Nov 28;81(11):C2630-C2638. Epub 2016 Sep 28.

Dept. of Food Processing and Preservation, Hajee Mohammad Danesh Science and Technology Univ, Dinajpur, Bangladesh.

Lycopene was extraction, isolation and purification using recrystallization, column chromatography, and preparative thin layer chromatography (TLC) methods as well as degradation kinetics of lycopene were studied at refrigerated temperature and room temperature for 3 wk from watermelon. Higher lycopene degradation was observed at refrigerated temperature as compared to ambient temperature throughout the storage periods. The highest amount of lycopene retained in recrystallization (101.69 μg/g) followed by column chromatography (18.20 μg/g) and preparative TLC (15.57 μg/g). Color parameters, half-life time (t ), and color retention (%R) were dependent on extraction, isolation, and purification methods and storage life. Recrystallization and preparative TLC were followed by first order reaction model. Preparative TLC exhibited higher activation energy than did the recrystallization and column chromatography. Therefore, the result shows that recrystallization method could apply to extract and purify lycopene from watermelon that would also be used as a natural colorant as well as value-added product.
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http://dx.doi.org/10.1111/1750-3841.13504DOI Listing
November 2016

Wettability of partially suspended graphene.

Sci Rep 2016 Apr 13;6:24237. Epub 2016 Apr 13.

Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY 11973, USA.

The dependence of the wettability of graphene on the nature of the underlying substrate remains only partially understood. Here, we systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Further, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquid interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle.
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http://dx.doi.org/10.1038/srep24237DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829856PMC
April 2016

Arbitrary lattice symmetries via block copolymer nanomeshes.

Nat Commun 2015 Jun 23;6:7448. Epub 2015 Jun 23.

Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA.

Self-assembly of block copolymers is a powerful motif for spontaneously forming well-defined nanostructures over macroscopic areas. Yet, the inherent energy minimization criteria of self-assembly give rise to a limited library of structures; diblock copolymers naturally form spheres on a cubic lattice, hexagonally packed cylinders and alternating lamellae. Here, we demonstrate multicomponent nanomeshes with any desired lattice symmetry. We exploit photothermal annealing to rapidly order and align block copolymer phases over macroscopic areas, combined with conversion of the self-assembled organic phase into inorganic replicas. Repeated photothermal processing independently aligns successive layers, providing full control of the size, symmetry and composition of the nanoscale unit cell. We construct a variety of symmetries, most of which are not natively formed by block copolymers, including squares, rhombuses, rectangles and triangles. In fact, we demonstrate all possible two-dimensional Bravais lattices. Finally, we elucidate the influence of nanostructure on the electrical and optical properties of nanomeshes.
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http://dx.doi.org/10.1038/ncomms8448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557284PMC
June 2015
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