bluuebunny/crossref_metadata_2025_split huggingface dataset:
Economic and biophysical limits to seaweed farming for climate change mitigation
Authors: DeAngelo Julianne , Saenz Benjamin T. , Arzeno-Soltero Isabella B. , Frieder Christina A. , Long Matthew C. , Hamman Joseph , Davis Kristen A. , Davis Steven J. 
Published: December 2022

AbstractNet-zero greenhouse gas (GHG) emissions targets are driving interest in opportunities for biomass-based negative emissions and bioenergy, including from marine sources such as seaweed. Yet the biophysical and economic limits to farming seaweed at scales relevant to the global carbon budget have not been assessed in detail. We use coupled seaweed growth and technoeconomic models to estimate the costs of global seaweed production and related climate benefits, systematically testing the relative importance of model parameters. Under our most optimistic assumptions, sinking farmed seaweed to the deep sea to sequester a gigaton of CO2 per year costs as little as US$480 per tCO2 on average, while using farmed seaweed for products that avoid a gigaton of CO2-equivalent GHG emissions annually could return a profit of $50 per tCO2-eq. However, these costs depend on low farming costs, high seaweed yields, and assumptions that almost all carbon in seaweed is removed from the atmosphere (that is, competition between phytoplankton and seaweed is negligible) and that seaweed products can displace products with substantial embodied non-CO2 GHG emissions. Moreover, the gigaton-scale climate benefits we model would require farming very large areas (>90,000 km2)—a >30-fold increase in the area currently farmed. Our results therefore suggest that seaweed-based climate benefits may be feasible, but targeted research and demonstrations are needed to further reduce economic and biophysical uncertainties.
Accelerating tobacco control at the national level with the Smoke-free Generation movement in the Netherlands
Authors: Willemsen Marc C. , Been Jasper V. 
Published: December 2022

AbstractThe Netherlands has moved towards the forefront of tobacco control in Europe, after having implemented important tobacco control measures in 2020 and 2021, which included higher tobacco taxation, plain packaging of tobacco products, a partial point of sale tobacco display ban, smoking ban on school grounds, and other smoking restrictions. We examined the factors contributing to these successes, focussing on the network of tobacco control advocacy organisations and the process of agenda-setting. Crucial determining factors were stricter adherence to Article 5.3 FCTC, which prevents government to consult tobacco industry, and the genesis of a ‘Smoke-free Generation’ movement in the wider society, initiated by the three main national charities (Lung Foundation Netherlands, Dutch Heart Foundation, Dutch Cancer Society). The Smoke-free Generation concept proved to be a highly attractive unifying strategy for national en local policy makers and Dutch society. As a result, the Dutch government was able to start a process of strengthening tobacco control policy through drafting and implementing a National Prevention Agreement, which aims at a tobacco control endgame goal of less than 5% smokers in 2040. Between 2019 and 2020 smoking rates dropped from 21.7% to 20.2%. The Dutch experience can provide inspiration for countries where tobacco control is still lagging behind. It also illustrates that continued vigilance is needed, since the most recent government change was associated with a hampering of further reduction of the proportion of smokers and a temporary drop in attention to tobacco control from the central government.
Neocortical synaptic engrams for remote contextual memories
Authors: Lee Ji-Hye , Kim Woong Bin , Park Eui Ho , Cho Jun-Hyeong 
Published: December 2022

AbstractWhile initial encoding of contextual memories involves the strengthening of hippocampal circuits, these memories progressively mature to stabilized forms in neocortex and become less hippocampus dependent. Although it has been proposed that long-term storage of contextual memories may involve enduring synaptic changes in neocortical circuits, synaptic substrates of remote contextual memories have been elusive. Here we demonstrate that the consolidation of remote contextual fear memories in mice correlated with progressive strengthening of excitatory connections between prefrontal cortical (PFC) engram neurons active during learning and reactivated during remote memory recall, whereas the extinction of remote memories weakened those synapses. This synapse-specific plasticity was CREB-dependent and required sustained hippocampal signals, which the retrosplenial cortex could convey to PFC. Moreover, PFC engram neurons were strongly connected to other PFC neurons recruited during remote memory recall. Our study suggests that progressive and synapse-specific strengthening of PFC circuits can contribute to long-term storage of contextual memories.
A novel feature for monitoring the enzymatic harvesting process of adherent cell cultures based on lens-free imaging
Authors: Deckers T. , Aerts J.-M. , Bloemen V. 
Published: December 2022

AbstractAdherent cell cultures are often dissociated from their culture vessel (and each other) through enzymatic harvesting, where the detachment response is monitored by an operator. However, this approach is lacking standardisation and reproducibility, and prolonged exposure or too high concentrations can affect the cell’s viability and differentiation potential. Quantitative monitoring systems are required to characterise the cell detachment response and objectively determine the optimal time-point to inhibit the enzymatic reaction. State-of-the-art methodologies rely on bulky imaging systems and/or features (e.g. circularity) that lack robustness. In this study, lens-free imaging (LFI) technology was used to develop a novel cell detachment feature. Seven different donors were cultured and subsequently harvested with a (diluted) enzymatic harvesting solution after 3, 5 and 7 days of culture. Cell detachment was captured with the LFI set-up over a period of 20 min (every 20 s) and by optimising the reconstruction of the LFI intensity images, a new feature could be identified. Bright regions in the intensity image were identified as detaching cells and using image analysis, a method was developed to automatically extract this feature, defined as the percentage of detached cell regions. Next, the method was quantitatively and qualitatively validated on a diverse set of images. Average absolute error values of 1.49%, 1.34% and 1.97% were obtained for medium to high density and overconfluent cultures, respectively. The detachment response was quantified for all conditions and the optimal time for enzyme inhibition was reached when approximately 92.5% of the cells were detached. On average, inhibition times of 9.6–11.1 and 16.2–17.2 min were obtained for medium to high density and overconfluent cultures, respectively. In general, overconfluent cultures detached much slower, while their detachment rate was also decreased by the diluted harvesting solution. Moreover, several donors exhibited similar trends in cell detachment behaviour, with two clear outliers. Using the novel feature, measurements can be performed with an increased robustness, while the compact LFI design could pave the way for in situ monitoring in a variety of culture vessels, including bioreactors.
A network approach for low dimensional signatures from high throughput data
Authors: Curti Nico , Levi Giuseppe , Giampieri Enrico , Castellani Gastone , Remondini Daniel 
Published: December 2022

AbstractOne of the main objectives of high-throughput genomics studies is to obtain a low-dimensional set of observables—a signature—for sample classification purposes (diagnosis, prognosis, stratification). Biological data, such as gene or protein expression, are commonly characterized by an up/down regulation behavior, for which discriminant-based methods could perform with high accuracy and easy interpretability. To obtain the most out of these methods features selection is even more critical, but it is known to be a NP-hard problem, and thus most feature selection approaches focuses on one feature at the time (k-best, Sequential Feature Selection, recursive feature elimination). We propose DNetPRO, Discriminant Analysis with Network PROcessing, a supervised network-based signature identification method. This method implements a network-based heuristic to generate one or more signatures out of the best performing feature pairs. The algorithm is easily scalable, allowing efficient computing for high number of observables ($$10^3$$

10
3

–$$10^5$$

10
5

). We show applications on real high-throughput genomic datasets in which our method outperforms existing results, or is compatible with them but with a smaller number of selected features. Moreover, the geometrical simplicity of the resulting class-separation surfaces allows a clearer interpretation of the obtained signatures in comparison to nonlinear classification models.
Paleoenvironmental changes in river channel systems in alpine rockslide deposits exemplified by the Fernpass rockslide in the Tyrolian Außerfern District, Austria
Authors: Wolkersdorfer Christian 
Published: December 2022

AbstractThis paper describes the instability of river channel systems in alpine rockslide deposits using the Fernpass Rockslide and the river Loisach in the Tyrolian Außerfern District (Austria) as an example of paleoenvironmental developments. This is the first investigation of this kind of the Fernpass, one of the most important Alpine north–south transport connections since the bronze age. It uses geomorphological, sedimentological, onomastic and hydrogeological investigations to reconstruct the course of a late Holocene river in this area and a probabilistic simulation for dating. Tracer tests assisted in investigating the potential groundwater connections of the river systems. The findings show that the Palaeoloisach runs on the orographically right side in a marginal valley of the Fernpass furrow and changes to the orographically left side of the furrow within the Rauth suburb in the village of Biberwier. A probabilistic simulation of the Narrenbichl slip event, which changed the course of the Palaeoloisach, dates the event to an age of 664 ± 116 BC. This investigation is an important contribution to understanding Quaternary postrockslide developments, how groundwater contributes to forming postrockslide channel systems and archaeological findings occurring in populated areas.
Assessing and removing the effect of unwanted technical variations in microbiome data
Authors: Fachrul Muhamad , Méric Guillaume , Inouye Michael , Pamp Sünje Johanna , Salim Agus 
Published: December 2022

AbstractVarying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze–thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of classBacteroidiathe most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.
Ionic liquid-loaded triazine-based magnetic nanoparticles for promoting multicomponent reaction
Authors: Kafshdarzadeh Kosar , Malmir Masoume , Amiri Zahra , Heravi Majid M. 
Published: December 2022

AbstractA novel hybrid magnetic ionic-liquid as a heterogeneous catalyst was synthesized by hybridization of imidazolium based-ionic liquid onto the nitrogen rich magnetic nanocomposite. The resulting catalyst (n-Fe3O4@SiO2-TA-SO3H IL) has two advantages besides recyclability: (i) high capacity of functional-SO3H group with imidazolium-IL cation for promoting symmetric and asymmetric Hantzsch reaction and (ii) easy recovery. Caused by the polymeric and magnetic nature of the n-Fe3O4@SiO2-TA-SO3H IL, large quantities of acidic groups were bound to the n-Fe3O4@SiO2-TA surface, which reduced the catalyst mass applied to the catalytic reaction. Moreover, superior catalytic performance and outstanding recyclability of n-Fe3O4@SiO2-TA-SO3H IL in mild condition make this method a green pathway for manufacture of satisfactory chemicals.
The role of discrimination in the relation between COVID-19 sequelae, psychological distress, and work impairment in COVID-19 survivors
Authors: Ishii Shinya , Sugiyama Aya , Ito Noriaki , Miwata Kei , Kitahara Yoshihiro , Okimoto Mafumi , Kurisu Akemi , Abe Kanon , Imada Hirohito , Akita Tomoyuki , Kubo Tatsuhiko , Nagasawa Akira , Nakanishi Toshio , Takafuta Toshiro , Kuwabara Masao , Tanaka Junko 
Published: December 2022

AbstractPerceived discrimination and work impairment are commonly observed in COVID-19 survivors, but their relationship has not been well understood. We aimed to evaluate the role of discrimination in the development of psychological distress and work impairment in COVID-19 survivors. From April 2020 to November 2021, 309 patients were recruited at two designated COVID-19 hospitals in Japan. Participants completed a standardized questionnaire including COVID-19 sequelae, psychological distress, impairments in work performance and perceived discrimination. The majority of participants (62.5%) experienced one or more COVID-19 sequelae. Psychological distress was observed in 36.9% and work impairment in 37.9%. In multivariate logistic regression analyses, COVID-19 sequelae and discrimination were associated with both psychological distress and work impairment. Mediation analysis demonstrated that the direct effect of sequelae on work impairment was non-significant after accounting for psychological distress, suggesting that the effect of sequelae on work impairment was mainly mediated through psychological distress. These findings were replicated in a subgroup analysis limited to patients with mild COVID-19. We conclude that discrimination plays an important role in the development of psychological distress and work impairment, and that both discrimination and psychological distress should be targets of intervention in COVID-19 survivors.
In silico activity and ADMET profiling of phytochemicals from Ethiopian indigenous aloes using pharmacophore models
Authors: Bultum Lemessa Etana , Tolossa Gemechu Bekele , Kim Gwangmin , Kwon Ohhyeon , Lee Doheon 
Published: December 2022

AbstractIn silico profiling is used in identification of active compounds and guide rational use of traditional medicines. Previous studies on Ethiopian indigenous aloes focused on documentation of phytochemical compositions and traditional uses. In this study, ADMET and drug-likeness properties of phytochemicals from Ethiopian indigenous aloes were evaluated, and pharmacophore-based profiling was done using Discovery Studio to predict therapeutic targets. The targets were examined using KEGG pathway, gene ontology and network analysis. Using random-walk with restart algorithm, network propagation was performed in CODA network to find diseases associated with the targets. As a result, 82 human targets were predicted and found to be involved in several molecular functions and biological processes. The targets also were linked to various cancers and diseases of immune system, metabolism, neurological system, musculoskeletal system, digestive system, hematologic, infectious, mouth and dental, and congenital disorder of metabolism. 207 KEGG pathways were enriched with the targets, and the main pathways were metabolism of steroid hormone biosynthesis, lipid and atherosclerosis, chemical carcinogenesis, and pathways in cancer. In conclusion, in silico target fishing and network analysis revealed therapeutic activities of the phytochemicals, demonstrating that Ethiopian indigenous aloes exhibit polypharmacology effects on numerous genes and signaling pathways linked to many diseases.
Ocean acidification causes fundamental changes in the cellular metabolism of the Arctic copepod Calanus glacialis as detected by metabolomic analysis
Authors: Thor Peter , Vermandele Fanny , Bailey Allison , Guscelli Ella , Loubet-Sartrou Léa , Dupont Sam , Calosi Piero 
Published: December 2022

AbstractUsing a targeted metabolomic approach we investigated the effects of low seawater pH on energy metabolism in two late copepodite stages (CIV and CV) of the keystone Arctic copepod species Calanus glacialis. Exposure to decreasing seawater pH (from 8.0 to 7.0) caused increased ATP, ADP and NAD+ and decreased AMP concentrations in stage CIV, and increased ATP and phospho-L-arginine and decreased AMP concentrations in stage CV. Metabolic pathway enrichment analysis showed enrichment of the TCA cycle and a range of amino acid metabolic pathways in both stages. Concentrations of lactate, malate, fumarate and alpha-ketoglutarate (all involved in the TCA cycle) increased in stage CIV, whereas only alpha-ketoglutarate increased in stage CV. Based on the pattern of concentration changes in glucose, pyruvate, TCA cycle metabolites, and free amino acids, we hypothesise that ocean acidification will lead to a shift in energy production from carbohydrate metabolism in the glycolysis toward amino acid metabolism in the TCA cycle and oxidative phosphorylation in stage CIV. In stage CV, concentrations of most of the analysed free fatty acids increased, suggesting in particular that ocean acidification increases the metabolism of stored wax esters in this stage. Moreover, aminoacyl-tRNA biosynthesis was enriched in both stages indicating increased enzyme production to handle low pH stress.
Insights into the deglacial variability of phytoplankton community structure in the eastern equatorial Pacific Ocean using [231Pa/230Th]xs and opal-carbonate fluxes
Authors: Schimmenti Danielle , Marcantonio Franco , Hayes Christopher T. , Hertzberg Jennifer , Schmidt Matthew , Sarao John 
Published: December 2022

AbstractFully and accurately reconstructing changes in oceanic productivity and carbon export and their controls is critical to determining the efficiency of the biological pump and its role in the global carbon cycle through time, particularly in modern CO2 source regions like the eastern equatorial Pacific (EEP). Here we present new high-resolution records of sedimentary 230Th-normalized opal and nannofossil carbonate fluxes and [231Pa/230Th]xs ratios from site MV1014-02-17JC in the Panama Basin. We find that, across the last deglaciation, phytoplankton community structure is driven by changing patterns of nutrient (nitrate, iron, and silica) availability which, in turn, are caused by variability in the position of the Intertropical Convergence Zone (ITCZ) and associated changes in biogeochemical cycling and circulation in the Southern Ocean. Our multi-proxy work suggests greater scrutiny is required in the interpretation of common geochemical proxies of productivity and carbon export in the EEP.
Colonocyte keratin 7 is expressed de novo in inflammatory bowel diseases and associated with pathological changes and drug-resistance
Authors: Polari Lauri , Tenhami Mervi , Anttila Santeri , Helenius Terhi , Kujari Harry , Kallajoki Markku , Voutilainen Markku , Toivola Diana M. 
Published: December 2022

AbstractThe clinical course of IBD, characterized by relapses and remissions, is difficult to predict. Initial diagnosis can be challenging, and novel disease markers are needed. Keratin 7 (K7) is a cytoskeletal intermediate filament protein not expressed in the colonic epithelium but has been reported in IBD-associated colorectal tumors. Our aim was to analyze whether K7 is expressed in chronic colonic inflammatory diseases and evaluate its potential as a novel biomarker. K7 was analyzed in two patient cohorts using immunohistochemistry-stained colon samples and single-cell quantitative digital pathology methods. K7 was correlated to pathological changes and clinical patient characteristics. Our data shows that K7 is expressed de novo in the colonic epithelium of ulcerative colitis and Crohn’s disease IBD patients, but not in collagenous or lymphocytic colitis. K7 mRNA expression was significantly increased in colons of IBD patients compared to controls when assessed in publicly available datasets. While K7 increased in areas with inflammatory activity, it was not expressed in specific crypt compartments and did not correlate with neutrophils or stool calprotectin. K7 was increased in areas proximal to pathological alterations and was most pronounced in drug-resistant ulcerative colitis. In conclusion, colonic epithelial K7 is neo-expressed selectively in IBD patients and could be investigated for its potential as a disease biomarker.
Galápagos tortoise stable isotope ecology and the 1850s Floreana Island Chelonoidis niger niger extinction
Authors: Conrad Cyler , Barceló Laura Pagès , Scheinberg Lauren , Campbell Patrick D. , Wynn Addison , Gibbs James P. , Aguilera Washington Tapia , Cayot Linda , Bruner Kale , Pastron Allen G. , Jones Emily Lena 
Published: December 2022

AbstractA consequence of over 400 years of human exploitation of Galápagos tortoises (Chelonoidis niger ssp.) is the extinction of several subspecies and the decimation of others. As humans captured, killed, and/or removed tortoises for food, oil, museums, and zoos, they also colonized the archipelago resulting in the introduction of invasive plants, animals, and manipulated landscapes for farming, ranching, and infrastructure. Given current conservation and revitalization efforts for tortoises and their habitats, here we investigate nineteenth and twentieth century Galápagos tortoise dietary ecology using museum and archaeological specimens coupled with analysis of carbon (δ13Ccollagen and δ13Capatite), nitrogen (δ15N), hydrogen (δD) and oxygen (δ18Oapatite) stable isotopes and radiocarbon dating. We identify that Galápagos tortoise diets vary between and within islands over time, and that long-term anthropogenic impacts influenced change in tortoise stable isotope ecology by using 57 individual tortoises from 10 different subspecies collected between 1833 and 1967—a 134-year period. On lower elevation islands, which are often hotter and drier, tortoises tend to consume more C4 vegetation (cacti and grasses). Our research suggests human exploitation of tortoises and anthropogenic impacts on vegetation contributed to the extinction of the Floreana Island tortoise (C. n. niger) in the 1850s.