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Article ; Online: Soluble Papain to Digest Monoclonal Antibodies; Time and Cost-Effective Method to Obtain Fab Fragment

Matthew Collins / Hanieh Khalili

Bioengineering, Vol 9, Iss 209, p

2022 Volume 209

Abstract: Antigen binding fragments (Fabs) used in research (e.g., antibody mimetics, antibody-drug conjugate, bispecific antibodies) are frequently obtained by enzymatic digestion of monoclonal antibodies using immobilised papain. Despite obtaining pure Fab, ... ...

Abstract	Antigen binding fragments (Fabs) used in research (e.g., antibody mimetics, antibody-drug conjugate, bispecific antibodies) are frequently obtained by enzymatic digestion of monoclonal antibodies using immobilised papain. Despite obtaining pure Fab, using immobilised papain to digest IgG has limitations, most notably slow digestion time (more than 8 h), high cost and limited scalability. Here we report a time and cost-effective method to produce pure, active and stable Fab using soluble papain. Large laboratory scale digestion of an antibody (100 mg) was achieved using soluble papain with a digestion time of 30 min and isolated yields of 55–60%. The obtained Fabs displayed similar binding activity as Fabs prepared via immobilised papain digestion. Site-specific conjugation between Fabs and polyethylene glycol (PEG) was carried out to obtain antibody mimetics FpF (Fab-PEG-Fab) indicating that the native disulphide bond had been preserved. Surface-plasmon resonance (SPR) of prepared FpFs showed that binding activity towards the intended antigen was maintained. We anticipate that this work will provide a fast and less costly method for researchers to produce antibody fragments at large scale from whole IgG suitable for use in research.
Keywords	papain ; IgG ; enzymatic digestion ; protein L purification ; Technology ; T ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Editorial

Chris Derksen / Carolina Adler / Matthew Collins / Zita Sebesvari

Frontiers in Climate, Vol

Knowledge gaps from the IPCC special report on the ocean and cryosphere in a changing climate and recent advances (volumes I and II)

2022 Volume 4

Keywords	cryosphere ; oceans ; Intergovernmental Panel on Climate Change (IPCC) ; knowledge gaps ; climate assessments ; mountains ; Environmental sciences ; GE1-350
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Heatwave–blocking relation change likely dominates over decrease in blocking frequency under global warming

Pak Wah Chan / Jennifer L. Catto / Matthew Collins

npj Climate and Atmospheric Science, Vol 5, Iss 1, Pp 1-

2022 Volume 8

Abstract: Abstract Extra-tropical continental summer heatwaves often occur under persistent anticyclones or blocking. Here we partition heatwave changes into contributions from blocking changes, heatwave–blocking relation change and mean temperature increase, ... ...

Abstract	Abstract Extra-tropical continental summer heatwaves often occur under persistent anticyclones or blocking. Here we partition heatwave changes into contributions from blocking changes, heatwave–blocking relation change and mean temperature increase, under global warming in climate models. We employ an optimized blocking index that best correlates with heatwaves (Pearson correlation of 0.7) and find heatwave-driving blocking decreases but the change in heatwave–blocking relation likely dominates. Over Europe, with a historical heatwave frequency of 2.5%, less blocking will cause 0.6% fewer heatwaves, steepened heatwave–blocking relation will cause 1.4% more heatwaves, and the mean temperature increase will cause 60% more heatwaves. Over Greenland, flattened heatwave–blocking relation will dominate over the insignificant decrease in blocking. The future increase in heatwave frequency is not caused by changes in blocking frequency, but by factors such as thermodynamics, that enhance the capacity of blocking to drive heatwaves.
Keywords	Environmental sciences ; GE1-350 ; Meteorology. Climatology ; QC851-999
Subject code	303
Language	English
Publishing date	2022-09-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Emerging Skill in Multi-Year Prediction of the Indian Ocean Dipole

F. Feba / Karumuri Ashok / Matthew Collins / Satish R. Shetye

Frontiers in Climate, Vol

2021 Volume 3

Abstract: The Indian Ocean Dipole is a leading phenomenon of climate variability in the tropics, which affects the global climate. However, the best lead prediction skill for the Indian Ocean Dipole, until recently, has been limited to ~6 months before the ... ...

Abstract	The Indian Ocean Dipole is a leading phenomenon of climate variability in the tropics, which affects the global climate. However, the best lead prediction skill for the Indian Ocean Dipole, until recently, has been limited to ~6 months before the occurrence of the event. Here, we show that multi-year prediction has made considerable advancement such that, for the first time, two general circulation models have significant prediction skills for the Indian Ocean Dipole for at least 2 years after initialization. This skill is present despite ENSO having a lead prediction skill of only 1 year. Our analysis of observed/reanalyzed ocean datasets shows that the source of this multi-year predictability lies in sub-surface signals that propagate from the Southern Ocean into the Indian Ocean. Prediction skill for a prominent climate driver like the Indian Ocean Dipole has wide-ranging benefits for climate science and society.
Keywords	Indian Ocean (Dipole) ; decadal prediction ; CanCM4 ; MIROC5 ; Southern Ocean ; IOD and Southern Ocean ; Environmental sciences ; GE1-350
Subject code	551
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Assessment of the Ability of CMIP6 GCMS to Simulate the Boreal Summer Intraseasonal Oscillation Over Southeast Asia

Abayomi A. Abatan / Matthew Collins / Mukand S. Babel / Dibesh Khadka / Yenushi K. De Silva

Frontiers in Climate, Vol

2021 Volume 3

Abstract: The boreal summer intraseasonal oscillation (BSISO) plays an important role in the intraseasonal variability of a wide range of weather and climate phenomena across the region modulated by the Asian summer monsoon system. This study evaluates the ... ...

Abstract	The boreal summer intraseasonal oscillation (BSISO) plays an important role in the intraseasonal variability of a wide range of weather and climate phenomena across the region modulated by the Asian summer monsoon system. This study evaluates the strengths and weaknesses of 19 Coupled Model Intercomparison Project Phase 6 (CMIP6) models to reproduce the basic characteristics of BSISO. The models' rainfall and largescale climates are evaluated against GPCP and ERA5 reanalysis datasets. All models exhibit intraseasonal variance of 30–60-day bandpass-filtered rainfall and convection anomalies but with diverse magnitude when compared with observations. The CMIP6 models capture the structure of the eastward/northward propagating BSISO at wavenumbers 1 and 2 but struggle with the intensity and location of the convection signal. Nevertheless, the models show a good ability to simulate the power spectrum and coherence squared of the principal components of the combined empirical orthogonal function (CEOF) and can capture the distinction between the CEOF modes and red noise. Also, the result shows that some CMIP6 models can capture the coherent intraseasonal propagating features of the BSISO as indicated by the Hovmöller diagram. The contribution of latent static energy to the relationship between the moist static energy and intraseasonal rainfall over Southeast Asia is also simulated by the selected models, albeit the signals are weak. Taking together, some of the CMIP6 models can represent the summertime climate and intraseasonal variability over the study region, and can also simulate the propagating features of BSISO, but biases still exist.
Keywords	CMIP6 ; BSISO simulation diagnostics ; intraseasonal variability ; MSE ; Southeast Asia ; Environmental sciences ; GE1-350
Subject code	551
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Which nursing home workers were at highest risk for SARS-CoV-2 infection during the November 2020–February 2021 winter surge of COVID-1?

Joseph Kellogg / William Dube / Carly Adams / Matthew Collins / Theodore Lopman / Theodore Johnson / Avnika Amin / Joshua Weitz / Scott Fridkin

Antimicrobial Stewardship & Healthcare Epidemiology, Vol 2, Pp s7-s

2022 Volume 7

Abstract: Background: Nursing home (NH) residents and staff were at high risk for COVID-19 early in the pandemic; several studies estimated seroprevalence of infection in NH staff to be 3-fold higher among CNAs and nurses compared to other staff. Risk mitigation ... ...

Abstract	Background: Nursing home (NH) residents and staff were at high risk for COVID-19 early in the pandemic; several studies estimated seroprevalence of infection in NH staff to be 3-fold higher among CNAs and nurses compared to other staff. Risk mitigation added in Fall 2020 included systematic testing of residents and staff (and furlough if positive) to reduce transmission risk. We estimated risks for SARS-CoV-2 infection among NH staff during the first winter surge before widespread vaccination. Methods: Between February and May 2021, voluntary serologic testing was performed on NH staff who were seronegative for SARS-CoV-2 in late Fall 2020 (during a previous serology study at 14 Georgia NHs). An exposure assessment at the second time point covered prior 3 months of job activities, community exposures, and self-reported COVID-19 vaccination, including very recent vaccination (≤4 weeks). Risk factors for seroconversion were estimated by job type using multivariable logistic regression, accounting for interval community-incidence and interval change in resident infections per bed. Results: Among 203 eligible staff, 72 (35.5%) had evidence of interval seroconversion (Fig. 1). Among 80 unvaccinated staff, interval infection was significantly higher among CNAs and nurses (aOR, 4.9; 95% CI, 1.4–20.7) than other staff, after adjusting for race and interval community incidence and facility infections. This risk persisted but was attenuated when utilizing the full study cohort including those with very recent vaccination (aOR, 1.8; 95% CI, 0.9–3.7). Conclusions: Midway through the first year of the pandemic, NH staff with close or common resident contact continued to be at increased risk for infection despite enhanced infection prevention efforts. Mitigation strategies, prior to vaccination, did not eliminate occupational risk for infection. Vaccine utilization is critical to eliminate occupational risk among frontline healthcare providers.
Keywords	Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	610
Language	English
Publishing date	2022-07-01T00:00:00Z
Publisher	Cambridge University Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Data From “A Biocodicological Analysis of the Medieval Library and Archive From Orval Abbey, Belgium”

Jorsua Herrera Bethencourt / Ismael Rodríguez Palomo / Simon Hickinbotham / Bharath Nair / Silvia Soncin / Marc Dieu / Matthew Collins / Olivier Deparis

Journal of Open Archaeology Data, Vol

2022 Volume 10

Abstract: The dataset contains the first-ever comprehensive biocodicological analysis of medieval library books and charters using Zooarchaeological Mass Spectrometry (ZooMS). Here, we analyze 68 codices and 59 charters (1490+59 samples in total) from one single ... ...

Abstract	The dataset contains the first-ever comprehensive biocodicological analysis of medieval library books and charters using Zooarchaeological Mass Spectrometry (ZooMS). Here, we analyze 68 codices and 59 charters (1490+59 samples in total) from one single monastic institution, namely the Cistercian abbey of Orval in present-day Belgium. The data entails both peptide mass fingerprinting (using MALDI-ToF) and peptide sequencing (using LC-MS/MS) analysis of almost the entire library and all the preserved single leaf charters from the monastery. MALDI-ToF data is stored in Zenodo – a multidisciplinary open access repository while the LC-MS/MS data is deposited in ProteomeXchange Consortium via PRIDE – a publicly available repository for MS-based proteomics data. Mass spectrometric data generated from an entire monastic library and archive is of immense value to integrate with multiple case studies aiming at understanding parchment production and use in medieval Europe. Paper linked with data: Ruffini-Ronzani, N., Nieus, J.F., Soncin, S., Hickinbotham, S., Dieu, M., Bouhy, J., Charles, C., Ruzzier, C., Falmagne, T., Hermand, X., Collins, M.J. and Deparis, O 2021. A biocodicological analysis of the medieval library and archive from Orval Abbey, Belgium. 'Royal Society Open Science, 8'(6), p.210210.
Keywords	manuscripts ; open science ; charters ; collagen ; parchment ; mass spectrometry ; open dataset ; open access ; liquid chromatography ; Archaeology ; CC1-960
Subject code	306
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Ubiquity Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Residential stock data and dataset on energy efficiency characteristics of residential building fabrics in Ireland

Tomás Mac Uidhir / Fionn Rogan / Matthew Collins / John Curtis / Brian Ó Gallachóir

Data in Brief, Vol 29, Iss , Pp - (2020)

2020

Abstract: These data support the research article “Improving energy savings from a residential retrofit policy: a new model to inform better retrofit decisions” – (Mac Uidhir et al., 2019) [1]. This article presents 3 data sources which are utilised in conjunction ...

Abstract	These data support the research article “Improving energy savings from a residential retrofit policy: a new model to inform better retrofit decisions” – (Mac Uidhir et al., 2019) [1]. This article presents 3 data sources which are utilised in conjunction with a detailed energy system model of the residential sector to explore policy pathways for residential retrofitting. Data is collected from the Central Statistics Office (CSO) and the Sustainable Energy Authority of Ireland (SEAI). The first SEAI dataset is compiled for Ireland in compliance with the EU Energy Performance of Buildings Directive (EPBD) [2]. Data is collected using the Dwelling Energy Assessment Procedure (DEAP) [3]. DEAP is used to produce energy performance certificates known as Building Energy Ratings (BER). A BER indicates a buildings energy performance across a 15-point energy efficiency scale, rated alphabetically from A1 to G, in units of kWh/m2 year. A BER is required for new buildings and the rent or sale of existing dwellings – therefore the database has consistently grown in size since its inception in 2006. The BER database contains 735,906 records of individual dwellings. The database includes detailed building fabric information across a range of different building types, year of construction, Main/Secondary space/water heating fuels, heating system efficiency, ventilation method and structure type (Insulated concrete form, Masonry, Timber or Steel Frame). The second SEAI dataset (PWBER) contains aggregated pre and post BER information for a sample of 112,007 dwellings retrofitted during the period 2010–2015; this database contains mean energy efficiency improvement (kWh/m2 year) for a range of retrofit combinations as they apply to nine distinct building archetypes. The third CSO dataset is compiled from census data, representing the frequency of building types by year of construction. Keywords: Residential energy efficiency database, Building energy rating, Energy performance certificates, Dwelling energy assessment procedure
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	690
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Editorial

Matthew Collins / Karumuri Ashok / Marcelo Barreiro / Mathew Koll Roxy / Sarah M. Kang / Thomas L. Frölicher / Guojian Wang / Renata Goncalves Tedeschi

Frontiers in Climate, Vol

New Techniques for Improving Climate Models, Predictions and Projections

2021 Volume 3

Keywords	climate ; predictions ; projections ; machine learning ; data assimilation ; uncertainties ; Environmental sciences ; GE1-350
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: CMIP5 Intermodel Relationships in the Baseline Southern Ocean Climate System and With Future Projections

Jules B. Kajtar / Agus Santoso / Matthew Collins / Andréa S. Taschetto / Matthew H. England / Leela M. Frankcombe

Earth's Future, Vol 9, Iss 6, Pp n/a-n/a (2021)

2021

Abstract: Abstract Climate models exhibit a broad range in the simulated properties of the climate system. In the early historical period, the absolute global mean surface air temperature in Coupled Model Intercomparison Project, Phase 5 (CMIP5) models spans a ... ...

Abstract	Abstract Climate models exhibit a broad range in the simulated properties of the climate system. In the early historical period, the absolute global mean surface air temperature in Coupled Model Intercomparison Project, Phase 5 (CMIP5) models spans a range of ∼12°C – 15°C. Other climate variables may be linked to global mean temperature, and so accurate representation of the baseline climate state is crucial for meaningful future climate projections. In CMIP5 baseline climate states, statistically significant intermodel correlations between Southern Ocean surface temperature, outgoing shortwave radiation, cloudiness, the position of the mid‐latitude eddy‐driven jet, and Antarctic sea ice area are found. The baseline temperature relationships extend to projected future changes in the same set of variables, impacting on the projected global mean surface temperature change. Models with initially cooler Southern Ocean tend to exhibit more global warming, and vice versa for initially warmer models. These relationships arise due to a “capacity for change”. For example, cold‐biased models tend to have more cloud cover, sea ice, and equatorward jet initially, and thus a greater capacity to lose cloud cover and sea ice, and for the jet to shift poleward under global warming. A first look at emerging data from CMIP6 reveals a shift of the relationship from the Southern Ocean towards the Antarctic region, possibly due to reductions in Southern Ocean biases, such as in westerly wind representation.
Keywords	Southern Ocean ; CMIP5 ; baseline climate ; climate sensitivity ; Environmental sciences ; GE1-350 ; Ecology ; QH540-549.5
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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