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Hindered rotor benchmarks for the transition states of free radical additions to unsaturated hydrocarbons
No full textThe hindered internal rotors of 32 transition states (TSs) formed through four free radicals, namely methyl, vinyl, ethyl, methoxy (CH3, C2H3, C2H5, CH3) additions to acetylene, ethylene, allene, propyne, and propene (C2H2/C2H4/C3H4-a/C3H4-p/C3H6) are studied. To validate the uncertainties of rate constants that stem from the use of different electronic structure methods to treat hindered rotors, the rotations of the newly formed C-C and/or C-O rotors in the transition states are calculated using commonly used DFT methods (B3LYP, M06-2X, omega B97X-D and B2PLYP-D3 with two Pople basis sets (6-31+G(d,p), 6-311++G(d,p)) and cc-pVTZ). The hindrance potential energies V(chi) calculated using the M06-2X/6-311++G(d,p) method are benchmarked at the CCSD(T), CCSD(T)-F12, DLPNO-CCSD(T) levels of theory with cc-pVTZ-F12 and cc-pVXZ (X = T, Q) basis sets and are extrapolated to the complete basis set (CBS) limit. The DLPNO-CCSD(T)/CBS method is proven to reproduce the CCSD(T)/CBS energies within 0.5 kJ mol(-1) and this method is selected as the benchmark for all of the rotors in this study. Rotational constants B(chi) are computed for each method based on the optimized geometries for the hindrance potential via the I(2,3) approximation. Thereafter, the V(chi) and B(chi) values are used to compute hindered internal rotation partition functions, Q(HR), as a function of temperature. The uncertainties in the V(chi), B(chi) and Q(HR) calculations stem from the use of different DFT methods for the internal rotor treatment are discussed for these newly formed rotors. For rotors formed by + C-2 alkenes/alkynes, the V(chi) and Q(HR) values calculated using DFT methods are compared with the DLPNO-CCSD(T)/CBS results and analysed according to reaction types. Based on comparisons of the DFT methods with the benchmarking method, reliable DFT methods are recommended for the treatment of internal rotors for different reaction types considering both accuracy and computational cost. This work, to the authors\u27 knowledge, is the first to systematically benchmark hindrance potentials which can be used to estimate uncertainties in theoretically derived rate constants arising from the choice of different electronic structure methods.Y. Sun and Q.-D. Wang would like to acknowledge financial funding by the China Scholarship Council (CSC). The authors want to acknowledge the financial support of Science Foundation Ireland under Grant No. 15/IA/3177. The Computational resources are provided by the Irish Centre for High-End Computing (ICHEC), under project number ngche063c, ngcom006c and ngche076c.2021-11-0
A review study of water quality index models and their use for assessing surface water quality
No full textThe water quality index (WQI) model is a popular tool for evaluating surface water quality. It uses aggregation techniques that allow conversion of extensive water quality data into a single value or index. Globally, the WQI model has been applied to evaluate water quality (surface water and groundwater) based on local water quality criteria. Since its development in the 1960s, it has become a popular tool due to its generalised structure and ease-of-use. Commonly, WQI models involve four consecutive stages; these are (1) selection of the water quality parameters, (2) generation of sub-indices for each parameter (3) calculation of the parameter weighting values, and (4) aggregation of sub-indices to compute the overall water quality index. Several researchers have utilized a range of applications of WQI models to evaluate the water quality of rivers, lakes, reservoirs, and estuaries. Some problems of the WQI model are that they are usually developed based on site-specific guidelines for a particular region, and are therefore not generic. Moreover, they produce uncertainty in the conversion of large amounts of water quality data into a single index.
This paper presents a comparative discussion of the most commonly used WQI models, including the different model structures, components, and applications. Particular focus is placed on parameterization of the models, the techniques used to determine the sub-indices, parameter weighting values, index aggregation functions and the sources of uncertainty. Issues affecting model accuracy are also discussed.The authors would like to acknowledge the Hardiman Research Scholarship of the National University of Ireland Galway, which funded the first author as part of his PhD program. The reserach was also supported by MaREI, the SFI Research Centre for Energy, Climate, and Marine [Grant No: 12/RC/2302_P2]
Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity
No full textA key effector route of the Sugar Code involves lectins that exert crucial regulatory controls by targeting distinct cellular glycans. We demonstrate that a¿¿single amino-acid substitution in a banana lectin, replacing histidine 84 with a threonine, significantly¿¿reduces its mitogenicity, while preserving its broad-spectrum antiviral potency. X-ray crystallography, NMR spectroscopy, and glycocluster assays reveal that loss of mitogenicity is strongly correlated with loss of pi-pi stacking between aromatic amino acids H84 and Y83, which removes a wall separating two carbohydrate binding sites, thus diminishing multivalent interactions. On the other hand, monovalent interactions and antiviral activity are preserved by retaining other wild-type conformational features and possibly through unique contacts involving the T84 side chain. Through such fine-tuning, target selection and downstream effects of a lectin can be modulated so as to knock down one activity, while preserving another, thus providing tools for therapeutics and for understanding the Sugar Code..The authors are grateful to Evelyn Coves-Datson, Anjan Saha, Dana Huskens,
Jen Lewis, and Dr. Derek Dube for assistance, Dr. David Smith of LS-CAT for
help with remote data collection, and Drs. B. Friday and A. Leddoz for inspiring
discussions. Work in the laboratories of D.M.M. and H.M.A-H. was supported
by an NIH grant (1R01CA144043). H.-J.G. was supported by the ECfunded GlycoHIT program (contract no. 260600) and Training Network
GLYCOPHARM (PITN-GA-2012-317297). M.D.S. and J.V.G. were supported
by grants from the NIH (AI096138, AI073146, and P30 AI50410). P.V.M. has
been supported by Marie Curie Intra-European Fellowships (500748,
514958, and 220948), the Programme for Research in Third-Level Institutions
(PRTLI), administered by the Higher Education Authority, the Irish Research
Council, Enterprise Ireland, and Science Foundation Ireland (04/BR/C0192,
06/RFP/CHO032, and 12/IA/1398). R.R. is grateful to the Natural Sciences
and Engineering Research Council of Canada (NSERC) for financial support
and for a Canadian Research Chair in Therapeutic Chemistry. The participation
of A. Papadopoulos and T.C. Shiao is also acknowledged in the preparation of
compounds 4–8. M.H.K. received support from the Concerned Parents for
AIDS Research. D.S. was supported by KU Leuven grants (GOA 10/014 and
PF 10/18), a European CHAARM grant (242135), and an equipment grant
from the Fondation Dormeur, Vaduz. Work in the laboratory of C.M.R. was supported in part by PHS grants (R01 AI099284, R01 AI072613, and R01CA057973). Work at the Utah State University was supported by a grant (contract number HHSN2722010000391/HHSN27200005/A37) from the Respiratory Diseases Branch, Division of Microbiology and Infectious Diseases,
NIAID, NIH. J.A.S., J.L.M, and H.M.A.-H. were partially supported by a grant
(P50 GM103297) from the NIH. J.A.S. and J.L.M were also supported in part
by the University of Michigan Center for Structural Biology. Use of the
Advanced Photon Source was funded by the U.S. Department of Energy (under contract no. DE-AC02-06CH11357), and use of the LS-CAT Sector 21 was
funded by the Michigan Economic Development Corporation and the Michigan
Technology Tri-Corridor (085P1000817). D.M.M. is the founder of Virule, a
company formed to commercialize H84T BanLec. This work is dedicated to
the memory
The regenerative capacity of bone tissue and autograft dust exposed to heat shock induced by high speed surgical cutting
No full textHigh speed surgical cutting tools induce heat (>47°C) for short durations on bone tissue, leading to a thermally-induced cell death in bone cells. Post-operative bone healing at the cut surface and bone dust are important for ensuring the success of surgery and preventing long recovery time for patients. Autograft bone dust prepared using surgical burs can be re-introduced into patients to enhance bone healing. Recent in vitro and in vivo studies have provided evidence that thermal elevations can in fact trigger osteogenic responses by bone cells, enhancing mineralisation and new bone formation. However, whether bone dust and the cut surface exhibit an osteogenic response to heat shock induced by cutting conditions is unknown. Moreover, the influence of cutting conditions on the osteogenic potential of bone dust is not understood. In particular, the influence of the tissue source, the design of the cutting tool and the use of irrigation have not been investigated. Thus, the global aim of this PhD Thesis is to assess the ex-vivo osteogenic potential of autograft bone dust and the cut surface resected under different cutting conditions, and associated temperature elevations, using surgical burs for cutting and heat induction.
The duration of bone surface exposure to elevated temperatures during surgical bone cutting and the extent of heat dissipation and its effect on the bone healing capacity are not well understood. The first study of this PhD thesis sought to address this gap by conducting experimental studies to determine (1) temperature generation and dissipation during surgical bone cutting with no irrigation and (2) the ex-vivo regenerative potential of bone dust and the cut surface. During surgical cutting of bovine bone using burs (Multi-Flute, 2Flute) the relative surface temperatures (using a thermal camera) and dissipated temperatures (measured by embedded thermocouples) were quantified. Ex-vivo culture of bone dust and the cut surface samples were conducted up to 20 days post-cutting. Histological staining and biochemical assays (Alamar Blue, ALP, Alizarin red staining) quantified osteonecrosis and osteogenesis. The results of this study revealed that superficial heat generation induced by high speed surgical burs for short durations triggered an osteogenic response in bone dust, which was associated with apoptotic cell death. The cutting temperature was significantly higher with the Multi-Flute compared to the 2Flute bur, but the % heated tissue volume was lower and faster cooling was observed. Interestingly, the ex-vivo osteogenic capacity of both the bone dust and the cut surface were enhanced when using the Multi-Flute bur, even though increased apoptotic thermal damage was observed.
To reduce the risk of excess tissue necrosis during surgical cutting, irrigation is commonly used to minimise temperature elevation. Yet, the influence of irrigation approaches, namely using a surgical assistant to apply irrigation (manual) or using an automated irrigation (continuous) device, have not been investigated and as such there is no consensus regarding a favourable approach to minimise tissue necrosis or osteogenesis. The objective of the second study was to determine how irrigation techniques influence cellular responses to surgical bone cutting. Specifically, this study sought to (1) compare superficial temperature generation and dissipation during high speed surgical bone cutting with either manual or continuous irrigation and (2) determine the influence of irrigation technique on the ex-vivo regenerative potential of bone dust and the cut surface. The results of this study revealed that dissipated temperatures remained below 30°C throughout the cutting for both types of irrigation. Interestingly, the cut surface was preserved when continuous irrigation was used during cutting. In contrast, when using manual irrigation increased apoptotic thermal damage was observed and the ex-vivo osteogenic capacity of bone dust was enhanced. This study can inform surgical irrigation approaches to preserve the osteogenic potential of bone dust and the cut surface.
The most common implantation site for such autografts is in the spine, where bone dust is subjected to in vivo biophysical conditions, including compression and torsional forces. However, previous studies of autograft bone dust have been conducted under static conditions and so the mineralisation potential of bone dust in a mechanical environment representative of in vivo conditions is unknown. The objective of the third study was to assess and compare ex-vivo osteogenesis by bone dust using a custom-made compression bioreactor to recreate in vivo mechanical stimulation. The effect of irrigation was assessed under both static and mechanical loading conditions. Interestingly, in this study a 3mm bur was used and the irrigation method (manual or continuous irrigation) did not influence the mineralisation potential of bone dust under either static or mechanically stimulated conditions. Here it is reported for the first time that the osteogenic capacity (in terms of viability and mineralisation responses) was significantly higher for mechanically stimulated bone dust when compared to those cultured under static conditions. These results suggest that the osteogenic potential of bone dust may be enhanced by the mechanical loading conditions that exist in vivo.
Together, these studies provide (1) an insight into the osteogenic response of bone tissue resected with different design burs and different irrigation approaches during cutting, and (2) uncovers how the mechanical environment that arises in vivo might influence the osteogenic capacity of autograft bone dust. The information elucidated from this body of work can inform future surgical instrument design to improve post-operative bone tissue regeneration.2023-01-0
Homeless experiences and support needs of transgender people: A systematic review of the international evidence
No full textAim: To examine the experiences and support needs of homeless transgender people by synthesizing the existing evidence.
Background: Transgender people face many challenges in society in terms of people\u27s knowledge, understanding and acceptance of a person\u27s gender identity. Evidence regarding the homelessness experiences and available supports to transgender people remains sparse.
Methods: A systematic review was undertaken and included qualitative and quantitative studies. A total of twelve papers were included in the review, utilizing the PRISMA method. Methodological quality was evaluated using the Mixed Methods Assessment Tool (MMAT).
Results: Following analysis, the themes that emerged were (a) pathways into homelessness, (b) experiences whilst homeless and (c) routes out of homelessness.
Conclusion: It has become increasingly clear that the distinct needs of this group are complex and multifaceted. In order to adequately address the issues and concerns comprehensively, coordinated and effective collaborations need to be in place.
Implications for nursing management: Clinical nurses need to recognize and respond to the distinct needs of trans homeless people. Nurse managers need to provide leadership to promote the needs of homeless trans people and ensure that policies and procedures are in place that are responsive to issues and concerns
Change gradually, then all at once: the general election of February 2020 in the Republic of Ireland
No full textThe full text of this article will not be available in ULIR until the embargo expires on the 26/04/2022At the general election of February 2020, Sinn Féin won a plurality of the vote in the Republic of Ireland for the first time. The party system remained highly fragmented and, with Fianna Fáil and Fine Gael refusing to enter government with Sinn Féin, government formation took a record 20 weeks. Those 20 weeks coincided with the emergence of the Covid-19 public health emergency in Europe. A minority caretaker government introduced significant policy measures to address the associated public health and economic crises. At the end of June, Fianna Fáil and Fine Gael entered government together for the first time, and the Green Party joined them in a three-party majority coalition. The government faces significant challenges resulting from Covid-19 and from the UK’s exit from the EU, and other policy problems including housing and healthcare
Identifying Hotspots of Transport Disadvantage and Car Dependency in Rural Ireland
No full textThis paper explores the concepts of car dependency and transport disadvantage and the correlation between them in rural Ireland as a means of highlighting incidences of possible forced car ownership with the use of Geographical Information Systems (GIS). Societal and cultural challenges associated with the prevalence of the private car as the primary or in some cases the only form of mobility for people living in rural areas are examined resulting in potential cases of forced car ownership (FCO). Those defined as being forced to own a car are those who may find themselves in circumstances with low transport accessibility and low income, which is intensified by the need to economically participate in society for financial gain . This paper examines the existing gap between the necessity of transport and the provision of reliable public transport in rural Ireland, which is frequently attributed as a major determinant of FCO in the literature. While it is acknowledged that forced car ownership similarly exists in urban areas under the same or similar conditions, this paper focuses exclusively on the incidence of FCO in rural areas due to potentially higher levels of car dependency. The main objective of this paper is to identify hotspots or areas that are susceptible to increasing rates of FCO and transport disadvantage. Using the information gained from identifying the locations of these hotspots, transport planners and policymakers can tailor interventions to improve sustainable mobility in these areas and address equity concerns
New analytical tools and frameworks to understand dementia: What can a human-rights lens offer?
No full textThe biomedical model has traditionally informed the dominant discourse on dementia and has significantly shaped practitioners’, policy makers’ and researchers’ responses. This model contextualises dementia as a progressive neuro-degenerative cognitive disorder and focuses on deficits and underlying pathology, often overlooking the fact that the person can and should be an active partner in the treatment process. Beginning in the late 1990s, the exclusive reliance on the bio-medical model has come under increasing scrutiny with a growing awareness that by recasting dementia in broader social and more humanitarian terms, much can be done to promote the individual\u27s quality of life. Different frameworks and analytical tools have been forwarded to help us better understand dementia. These include personhood, citizenship, public health, disability and human rights. This review examines the merits of framing dementia as a disability, a citizenship concern and a human rights issue. It highlights some of the potential gains that can arise for the individual in using a human rights model to enhance practice, inform policy and create a more balanced research agenda. The article concludes by arguing that the complexities and magnitude of dementia are such that it requires multiple responses and a broad range of interpretative frameworks
Participant characteristics are poorly reported in exercise trials in tendinopathy: A systematic review
No full textObjective: To evaluate the reporting of eligibility criteria and baseline participant characteristics in randomised controlled trials investigating the effects of exercise interventions in tendinopathy. Methods: Randomised controlled trials investigating the effects of exercise therapy compared to a nonexercising intervention in upper and lower limb tendinopathy were included. Data extraction was categorised into the following
domains: participant demographics, tendinopathy descriptors, general health, participant recruitment and eligibility criteria. Results: The review included the following tendinopathies: Achilles (n ¼ 9), gluteal (n ¼ 2), lateral elbow tendinopathy (n ¼ 15), patellar (n ¼ 3) plantar (n ¼ 3), and rotator cuff (n ¼ 13). Age, sex, duration of symptoms and symptom severity were commonly reported across the review, while prior history of
tendinopathy was poorly reported (6/45). Variables such as physical activity level (17/45), sleep (0/45), psychological factors (2/45), medication at baseline (8/45), co morbid health complaints (10/45) and sociodemographic factors (11/45) were poorly reported across the included studies. Substantial variation existed between studies in the specific eligibility criteria used. Conclusion: The findings of this systematic review demonstrate that participant characteristics are poorly reported in exercise trials in tendinopathy. To improve effectiveness of exercise interventions in tendinopathy, improved reporting of participan