Digital Commons Network^™

A Multilayer Exponential Random Graph Modelling Approach For Weighted Networks, Alberto Caimo, Isabella Gollini

Articles

A new modelling approach for the analysis of weighted networks with ordinal/polytomous dyadic values is introduced. Specifically, it is proposed to model the weighted network connectivity structure using a hierarchical multilayer exponential random graph model (ERGM) generative process where each network layer represents a different ordinal dyadic category. The network layers are assumed to be generated by an ERGM process conditional on their closest lower network layers. A crucial advantage of the proposed method is the possibility of adopting the binary network statistics specification to describe both the between-layer and across-layer network processes and thus facilitating the interpretation of the …

Spent Coffee Waste As A Potential Media Component For Xylanase Production And Potential Application In Juice Enrichment, Rajeev Ravindran, Gwilym Williams, Amit Jaiswal

Articles

In this study, spent coffee waste (SCW) was used as the sole carbon source for xylanase production in solid state fermentation mode using Aspergillus niger. A Box–Behnken design was constructed using three parameters viz. temperature, initial moisture content, and log number of sporestodeterminetheoptimalfermentationcondition. Thebestfermentationconditionsforxylanase productionwerefound to beincubation at30◦Cwith aninitial moisture contentof 70%and usingan inoculum of 6.5×106 spores/g of dry SCW. Furthermore, the design of experiments revealed that maintaining a medium composition of 0.2 g of yeast extract, 0.04 g of K2HPO4, and 0.03 g of MgSO4 increased xylanase production. Under optimised solid-state fermentation conditions an enzyme activity of 6495.6 IU/g …

Targeting Lipoprotein Biogenesis: Considerations Towards Antimicrobials, Toufic El Arnaout, Tewfic Soulimane

Articles

Decades have passed without approval of a new antibiotic class. Several companies have recently halted related discovery efforts because of multiple obstacles. One promising route under research is to target the lipoprotein maturation pathway in light of major recent findings and the virulence roles of lipoproteins. To support the future design of selective drugs, considerations and priority-setting are established for the main lipoprotein processing enzymes (Lgt, LspA, and Lnt) based on microbiology, biochemistry, structural biology, chemical design, and pharmacology. Although not all bacterial species will be similarly impacted by drug candidates, several advantages make LspA a top target to pursue …

Comparison Of Amblyopia In Schoolchildren In Ireland And Northern Ireland: A Population-Based Observational Cross-Sectional Analysis Of A Treatable Childhood Visual Deficit, Síofra Harrington, Karen Breslin, Veronica O'Dwyer, Kathryn Saunders

Articles

Objectives This study reports the prevalence of persistent amblyopia (post-traditional treatment age) in schoolchildren in the Republic of Ireland (henceforth Ireland) and Northern Ireland (NI), UK; populations with broadly similar refractive and genetic profiles but different eye-care systems. Design This is a population-based observational study of amblyopia and refractive error. Setting Recruitment and testing in primary and postprimary schools in Ireland and NI. Participants Two groups identified through random cluster sampling to represent the underlying population; Ireland 898 participants (12–13 years old) and NI 723 participants (295 aged 9–10 years old, 428 aged 15– 16 years old). Main outcome measures …

Low-Resolution Models For The Interaction Dynamics Of Coated Gold Nanoparticles With Β2-Microglobulin, Giorgia Brancolini, Hender Lopez, Stefano Corni, Valentina Tozzini

Articles

A large number of low-resolution models have been proposed in the last decades to reduce the computational cost of molecular dynamics simulations for bio-nano systems, such as those involving the interactions of proteins with functionalized nanoparticles (NPs). For the proteins, “minimalist” models at the one-bead-per residue (Cα-based) level and with implicit solvent are well established. For the gold NPs, widely explored for biotechnological applications, mesoscale (MS) models treating the NP core with a single spheroidal object are commonly proposed. In this representation, the surface details (coating, roughness, etc.) are lost. These, however, and the specificity of the functionalization, have been …

Risk Factors Associated With Myopia In Schoolchildren In Ireland, Síofra Harrington, Jim Stack, Veronica O'Dwyer

Articles

Aim To examine the demographic and social factors associated with myopia in schoolchildren in Ireland.

Methods Thirty-seven schools participated, representing a mix of urban and rural schools and schools in socioeconomically disadvantaged and non-disadvantaged areas in Ireland. Examination included cyclopleged autorefraction (1% cyclopentolate hydrochloride). Height and weight of participants were measured. Parents filled in a participant’s lifestyle questionnaire, including questions on daily screen time use and daylight exposure. Myopia was defined as spherical equivalent ≤−0.50 D.

Results Data from 1626 participants (881 boys, 745 girls) in two age groups, 6–7 years (728) and 12–13 years (898), were examined. Myopia prevalence …

Comparison Of Amblyopia In Schoolchildren In Ireland And Northern Ireland: A Population-Based Observational Cross-Sectional Analysis Of A Treatable Childhood Visual Deficit, Síofra Harrington, Karen Breslin, Veronica O'Dwyer, Kathryn Saunders

Articles

Objectives This study reports the prevalence of persistent amblyopia (post-traditional treatment age) in schoolchildren in the Republic of Ireland (henceforth Ireland) and Northern Ireland (NI), UK; populations with broadly similar refractive and genetic profiles but different eye-care systems.

Design This is a population-based observational study of amblyopia and refractive error.

Setting Recruitment and testing in primary and post-primary schools in Ireland and NI.

Participants Two groups identified through random cluster sampling to represent the underlying population; Ireland 898 participants (12–13 years old) and NI 723 participants (295 aged 9–10 years old, 428 aged 15–16 years old).

Main outcome measures Monocular …

Surface Modification Of Silver Nanoparticle (Agnp) By Liposomal Encapsulation Mitigates Agnp-Induced Inflammation, Azeez O. Yusef, Alan Casey

Articles

Silver nanoparticles (AgNP) are widely used in a variety of consumable products as antibacterial to prevent or treat infection. Unfortunately, evidence exits that AgNP induces inflammation which can worsen with repeated human exposure. However, there is little or no research on how to mitigate these adverse effects due to AgNP induced-toxicity. Here, we investigated if surface modification of AgNP by liposomal encapsulation suppresses AgNP-mediated inflammatory responses in THP1 monocytes and THP1 differentiated macrophages (TDM). AgNP was encapsulated in a dipalmitoyl phosphatidyl choline- (DPPC)/cholesterol-based liposome by extrusion through a 100-nm polycarbonate membrane to form Lipo-AgNP. It was found as expected that …

A Multiscale Model Of Protein Adsorption On A Nanoparticle Surface, David Power, Ian Rouse, Stefano Poggio, Erik Brandt, Hender Lopez, Alexander Lyubartsev, Vladimir Lobaskin

Articles

We present a methodology to quantify the essential interactions at the interface between inorganic solid nanoparticles (NPs) and biological molecules. Our model is based on pre-calculation of the repetitive contributions to the interaction from molecular segments, which allows us to efficiently scan a multitude of molecules and rank them by their adsorption affinity. The interaction between the biomolecular fragments and the nanomaterial are evaluated using a systematic coarse-graining scheme starting from all-atom molecular dynamics simulations. The NPs are modelled using a two-layer representation, where the outer layer is parameterized at the atomistic level and the core is treated at the …

Synchrotron Macro Atr-Ftir Microspectroscopy For High Resolution Chemical Mapping Of Single Cells, Jitraporn Vongsvivut, David Perezguaita, Bayden Wood, Phil Heraud, Karina Khambatta, David Hartnell, Mark J. Hackett, Mark J. Tobin

Articles

Attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy has been used widely for probing the molecular properties of materials. Coupling a synchrotron infrared (IR) beam to an ATR element using a high numerical aperture (NA) microscope objective enhances the spatial resolution, relative to transmission or transflectance microspectroscopy, by a factor proportional to the refractive index (n) of the ATR element. This work presents the development of the synchrotron macro ATR-FTIR microspectroscopy at Australian Synchrotron Infrared Microspectroscopy (IRM) Beamline, and demonstrates that high quality FTIR chemical maps of single cells and tissues can be achieved at an enhanced spatial …

Ocular Biometry, Refraction And Time Spent Outdoors During Daylight In Irish Schoolchildren, Síofra Harrington, Veronica O'Dwyer

Articles

Background: Previous studies have investigated the relationship between ocular biometry and spherical equivalent refraction in children. This is the first such study in Ireland. The effect of time spent outdoors was also investigated.

Methods: Examination included cycloplegic autorefraction and non-contact ocular biometric measures of axial length, corneal radius and anterior chamber depth from 1,626 children in two age groups: six to seven years and 12 to 13 years, from 37 schools. Parents/guardians completed a participant questionnaire detailing time spent outdoors during daylight in summer and winter.

Results: Ocular biometric data were correlated with spherical equivalent refraction (axial …

Two-Dimensional Correlation Analysis Of Raman Microspectroscopy Of Subcellular Interactions Of Drugs In Vitro, Hugh Byrne, Franck Bonnier, Zeineb Farhane

Articles

Two-dimensional (2D) correlation analysis is explored to data mine the time evolution of the characteristic Raman microspectroscopic signatures of the subcellular responses of the nucleoli of human lung cancer cells to the uptake of doxorubicin. A simulated dataset of experimental control spectra, perturbed with systematically time-dependent spectral changes, constituted by a short-term response which represents the initial binding of the drug in the nucleolus, followed by a longer term response of the organelle metabolism, is used to validate the analysis protocol. Applying 2D correlation analysis, the in phase, synchronous correlation coefficients are seen to contain contributions of both response profiles, …

Raman Spectroscopic Analysis Of Saliva For The Diagnosis Of Oral Cancer: A Systematic Review, Genecy Calado, Isha Behl, Amuthachelvi Daniel, Hugh Byrne, Fiona Lyng

Articles

Abstract Oral squamous cell carcinoma (OSCC) is one of the most common malignancies worldwide, and new protocols for routine and early detection are required. Raman spectroscopy is an optical based method that can provide sensitive and non-invasive real time detailed information on the biochemical content of a sample like saliva, through the unique vibrations of its constituent molecules and this is sensitive to changes associated with disease. A comprehensive systematic review of the available scientific literature related to Raman spectroscopy of human saliva for diagnosis of OSCC was performed. The 785 nm laser line was most applied wavelength along with …

Principal Components Analysis Of Raman Spectral Data For Screening Of Hepatitis C Infection, A. Dita, H. Nawaz, T. Mahmood, M. Tahir, N. Rashid, Muhammad Mudassar, A.A.H. Alsaadi, Hugh Byrne

Articles

In the current study, Raman spectroscopy is employed for the identification of the biochemical changes taking place during the development of Hepatitis C. The Raman spectral data acquired from the human blood plasma samples of infected and healthy individuals is analysed by Principal Components Analysis and the Raman spectral markers of the Hepatitis C Virus (HCV) infection are identified. Spectral changes include those associated with nucleic acidsat720 cm−1, 1077 cm−1 1678 (CO stretching mode of dGTP of RNA), 1778 cm−1 (RNA), with proteins at 1641 cm−1(amide-I), 1721 cm−1(CC stretching of proteins) and lipids at 1738 cm−1(CO of ester group in …

Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan

Articles

Objective: This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment.

Results: It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases.

Conclusion: Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed …

Arrows In Biology: Lack Of Clarity And Consistency Points To Confusion For Learners, Leslie Kate Wright, Jordan J. Cardenas, Phyllis Liang, Dina L. Newman

Articles

In this article, we begin to unpack the phenomenon of representational competence by ex¬ploring how arrow symbols are used in introductory biology textbook figures. Out of 1214 figures in an introductory biology textbook, 632 (52%) of them contained arrows that were used to represent many different concepts or processes. Analysis of these figures revealed little correlation between arrow style and meaning. A more focused study of 86 figures containing 230 arrows from a second textbook showed the same pattern of inconsistency. Interviews with undergraduates confirmed that arrows in selected textbook figures were confusing and did not readily convey the information …

The Goldilocks Approach: A Review Of Employing Design Of Experiments In Prokaryotic Recombinant Protein Production, Barry Ryan, Albert Uhoraningoga, Gemma K. Kinsella, Gary T. .. Henehan

Articles

The production of high yields of soluble recombinant protein is one of the main objectives of protein biotechnology. Several factors, such as expression system, vector, host, media composition and induction conditions can influence recombinant protein yield. Identifying the most important factors for optimum protein expression may involve significant investment of time and considerable cost. To address this problem statistical models, such as Design of Experiments (DoE), have been used to optimise recombinant protein production. This review explores the application of DoE in the production of recombinant proteins, focusing on prokaryotic expression systems with a specific emphasis on media composition and …

Risks Of Excess Iodine Intake In Ghana: Current Situation, Challenges, And Lessons For The Future, Brenda A.Z. Abu, Wilna Oldewage‐Theron,, Richmond N.O. Aryeetey

Articles

In Ghana, iodine deficiency was first reported in 1994 among 33% of the population. A nationwide Universal Salt Iodization (USI) program plus other complementary interventions were subsequently implemented as a response. Our paper reviews the current risks of excess iodine status in Ghana and identifies policy and research gaps. A mixed methods review of 12 policies and institutional reports and 13 peer‐reviewed articles was complemented with consultations with 23 key informants (salt producers and distributors, food processors, regulatory agency officials, and healthcare providers) purposively sampled between May and August 2017. The findings show a strong policy environment indicated by regulations …

Regeneration Of Aged Dmf For Use In Solid-Phase Peptide Synthesis, Jordan K. Magtaan, Marc Devocelle, Fintan Kelleher

Articles

DMF, which is still the most commonly used solvent for Fmoc-SPPS, has the potential for degradation over time on exposure to air (and water vapour) and storage, to give dimethylamine and formic acid impurities. In particular, dimethylamine can lead to unwanted deprotection of the Fmoc group during for example the initial loading of Fmoc amino acids in SPPS, which leads reduced calculated loading values. We have found that treatment of such aged DMF by simple sparging with an inert gas (N₂), or vacuum sonication, can regenerate the DMF in order to restore loading levels back to those found …

Eros And Polemos: Eroticized Combat In The Trojan War Myth, John Dayton

Articles

The connections between belligerence and sexuality are well known to ethologists and anthropologists and have received some attention in literary analysis. This study examines the Trojan War, in the mythical matter itself and in its treatment by Homer, as a figurative amatory conquest. We note first the element of female eroticism in the background: the war begins with a beauty contest and Helen’s abduction, and Homer’s Iliad begins in a symmetrical pattern with a quarrel over desirable captive women. These events reflect a primal relationship between combat and access to females. But we also notice that the Trojan males are …

Use Of Auto-Germ To Model Germination Timing In The Sagebrush-Steppe, William C. Richardson, Dallin R. Whitaker, Kyler P. Sant, Nicholas S. Barney, Ryan S. Call, Bruce A. Roundy, Zachary T. Aanderud, Matthew D. Madsen

Articles

Germination timing has a strong influence on direct seeding efforts, and therefore is a closely tracked demographic stage in a wide variety of wildland and agricultural settings. Predictive seed germination models, based on soil moisture and temperature data in the seed zone are an efficient method of estimating germination timing. We utilized Visual Basic for Applications (VBA) to create Auto‐Germ, which is an Excel workbook that allows a user to estimate field germination timing based on wet‐thermal accumulation models and field temperature and soil moisture data. To demonstrate the capabilities of Auto‐Germ, we calculated various germination indices and modeled germination …

Law & Laundry: White Laundresses, Chinese Laundrymen, And The Origins Of Muller V. Oregon, Emily Prifogle

Articles

This article uses the historian’s method of micro-history to rethink the significance of the Supreme Court decision Muller v. Oregon (1908). Typically considered a labor law decision permitting the regulation of women’s work hours, the article argues that through particular attention to the specific context in which the labor dispute took place — the laundry industry in Portland, Oregon — the Muller decision and underlying conflict should be understood as not only about sex-based labor rights but also about how the labor of laundry specifically involved race-based discrimination. The article investigates the most important conflicts behind the Muller decision, namely …

A Review On Bioconversion Of Agro-Industrial Wastes To Industrially Important Enzymes, Rajeev Ravindran, Shady S. Hassan, Gwilym A. Williams, Amit K, Jaiswal

Articles

Agro-industrial waste is highly nutritious in nature and facilitates microbial growth. Most agricultural wastes are lignocellulosic in nature; a large fraction of it is composed of carbohydrates. Agricultural residues can thus be used for the production of various value-added products, such as industrially important enzymes. Agro-industrial wastes, such as sugar cane bagasse, corn cob and rice bran, have been widely investigated via different fermentation strategies for the production of enzymes. Solid-state fermentation holds much potential compared with submerged fermentation methods for the utilization of agro-based wastes for enzyme production. This is because the physical–chemical nature of many lignocellulosic substrates naturally …

Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh Byrne, Alan Casey

Articles

The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium …

Confirmation Of Qtl That Underlie Resistance To Soybean Sudden Death Syndrome Using Nils And Snps, David A. Lightfoot, Yi Chen Lee, M Javed Iqbal, Victor Njiti, Stella K. Kantartzi, Paul Gibson, James Anderson

Articles

Soybean (Glycine max (L.) Merr.) cultivars differ in their resistance to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki). Breeding for improving SDS response has been challenging, due to the large number of known resistance loci (more than 43) and interactions among them. The aims here were to compare the inheritance of resistance to SDS in a near isogenic line (NIL) population that was fixed for 91.5% of the genome but appeared to segregated at loci underlying partial resistance to SDS; to examine the interaction with the loci; and to identify regions containing candidate genes underlying QTL. Used were; …

Combining Ontologies And Open Standards To Derive A Middle Layer Information Model For Interoperability Of Personal And Electronic Health Records, Dympna O'Sullivan, Panagiotis Plastiras

Articles

Objectives: To enable better interoperability between Personal Health Record (PHR) and Electronic Health Record (EHR) systems to allow exchange of data from patients to providers and vice versa in order to encourage PHR use and patient self-management. Methods: A non-binding middleware based on open technologies and standards that resides between a PHR and EHR system has been developed. Specifically, the middleware consists of an ontology-driven information model based on the HL7 Reference Information Model (RIM) and a set of transformation rules that work in conjunction with the information model to process data exported from a PHR or EHR system and …

Universities: The Fallen Angels Of Bayh-Dole?, Rebecca S. Eisenberg, Robert Cook-Deegan

Articles

The Bayh-Dole Act of 1980 established a new default rule that allowed nonprofit organizations and small businesses to own, as a routine matter, patents on inventions resulting from research sponsored by the federal government. Although universities helped get the Bayh-Dole Act through Congress, the primary goal, as reflected in the recitals at the beginning of the new statute, was not to benefit universities but to promote the commercial development and utilization of federally funded inventions. In the years since the passage of the Bayh-Dole Act, universities seem to have lost sight of this distinction. Their behavior as patent seekers, patent …

Physical Models Can Provide Superior Learning Opportunities Beyond The Benefits Of Active Engagements, Dina L. Newman, Megan Stefkovich, Catherine Clasen, Margaret A. Franzen, Leslie Kate Wright

Articles

The essence of molecular biology education lies in understanding of gene expression, with subtopics including the central dogma processes, such as transcription and translation. While these concepts are core to the discipline, they are also notoriously difficult for students to learn, probably because they cannot be directly observed. While nearly all active learning strategies have been shown to improve learning compared with passive lectures, little has been done to compare different types of active learning. We hypothesized that physical models of central dogma processes would be especially helpful for learning, because they provide a resource that students can see, touch, …

When Law Calls, Does Science Answer? A Survey Of Distinguished Scientists & Engineers, Shari Seidman Diamond, Richard O. Lempert

Articles

Sound legal decision-making frequently requires the assistance of scientists and engineers. The survey we conducted with the cooperation of the American Academy examines the views of the legal system held by some of the nation’s most distinguished scientists and engineers, what motivates them to participate or to refuse to assist in lawsuits when asked, and their assessment of their experiences when they do participate. The survey reveals that a majority of the responding scientists and engineers will agree to participate when asked, and when they turn down requests, the most common reasons are lack of time and absence of relevant …

Theobromine And Related Methylxanthines As Inhibitors Of Primary Amine Oxidase, Padraig Shanahan, Jeffrey O’Sullivan, Keith Tipton, Gemma Kinsella, Barry Ryan, Gary Henehan

Articles

Methylxanthines are the most widely consumed drugs in the world and evidence of their health benefits has been growing in recent years. Primary Amine Oxidase (PrAO) has been recognised as a therapeutic target for amelioration of inflammatory, vascular and neurodegenerative diseases. Previous work in our laboratories showed that caffeine inhibited Bovine PrAO with a Ki of 1.0mM using benzylamine as substrate.

This study aimed to extend our previous work and explore the possibility that related methylxanthines might influence PrAO activity. While paraxanthine, theophylline and 7-methylxanthine had little effect on PrAO, theobromine was a noncompetitive inhibitor with a Ki of 276±44µM. …