bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex genotyping method to validate the multiallelic genome editing outcomes using machine learning-assisted long-read sequencing
Authors: Kuno Akihiro , Ikeda Yoshihisa , Ayabe Shinya , Kato Kanako , Sakamoto Kotaro , Suzuki Sayaka , Morimoto Kento , Wakimoto Arata , Mikami Natsuki , Ishida Miyuki , Iki Natsumi , Hamada Yuko , Takemura Megumi , Daitoku Yoko , Tanimoto Yoko , Huong Dinh Tra Thi , Murata Kazuya , Hamada Michito , Muratani Masafumi , Yoshiki Atsushi , Sugiyama Fumihiro , Takahashi Satoru , Mizuno Seiya 
Published: December 2020

ABSTRACTGenome editing can introduce designed mutations into a target genomic site. Recent research has revealed that it can also induce various unintended events such as structural variations, small indels, and substitutions at, and in some cases, away from the target site. These rearrangements may result in confounding phenotypes in biomedical research samples and cause a concern in clinical or agricultural applications. However, current genotyping methods do not allow a comprehensive analysis of diverse mutations for phasing and mosaic variant detection. Here, we developed a genotyping method with an on-target site analysis software named Determine Allele mutations and Judge Intended genotype by Nanopore sequencer (DAJIN) that can automatically identify and classify both intended and unintended diverse mutations, including point mutations, deletions, inversions, and cis double knock-in at single-nucleotide resolution. Our approach with DAJIN can handle approximately 100 samples under different editing conditions in a single run. With its high versatility, scalability, and convenience, DAJIN-assisted multiplex genotyping may become a new standard for validating genome editing outcomes.
High-Throughput Developability Assays Enable Library-Scale Identification of Producible Protein Scaffold Variants
Authors: Golinski Alexander W. , Mischler Katelynn M. , Laxminarayan Sidharth , Neurock Nicole , Fossing Matthew , Pichman Hannah , Martiniani Stefano , Hackel Benjamin J. 
Published: December 2020

AbstractProteins require high developability - quantified by expression, solubility, and stability - for robust utility as therapeutics, diagnostics, and in other biotechnological applications. Measuring traditional developability metrics is low-throughput in nature, often slowing the developmental pipeline. We evaluated the ability of three high-throughput developability assays to predict the bacterial recombinant expression of paratope variants of the protein scaffold Gp2. Enabled by a phenotype/genotype linkage, assay performance for 105variants was calculated via deep sequencing of populations sorted by proxied developability. We trained a random forest model that predicts expression from assay performance that is 35% closer to the experimental variance and trains 80% more efficiently than a model predicting from sequence information alone. Utilizing the predicted expression, we performed a sitewise analysis and predicted mutations consistent with enhanced developability. The validated assays offer the ability to identify developable proteins at unprecedented scales, reducing the bottleneck of protein commercialization.
Analysis of the intracellular traffic of IgG in the context of Down syndrome (trisomy 21)
Authors: Cejas RB , Tamaño-Blanco M , Blanco JG 
Published: December 2020

AbstractPersons with Down syndrome (DS, trisomy 21) have widespread cellular protein trafficking defects. There is a paucity of data describing the intracellular transport of IgG in the context of endosomal-lysosomal alterations linked to trisomy 21. In this study, we analyzed the intracellular traffic of IgG mediated by the human neonatal Fc receptor (FcRn) in fibroblast cell lines with trisomy 21. Intracellular IgG trafficking studies in live cells showed that fibroblasts with trisomy 21 exhibit higher proportion of IgG in lysosomes (~10% increase), decreased IgG content in intracellular vesicles (~9% decrease), and a trend towards decreased IgG recycling (~55% decrease) in comparison to diploid cells. Amyloid-beta precursor protein (APP) overexpression in diploid fibroblasts replicated the increase in IgG sorting to the degradative pathway observed in cells with trisomy 21. The impact ofAPPon the expression ofFCGRT(alpha chain component of FcRn) was investigated byAPPknock down and overexpression of the APP protein.APPknock down increased the expression ofFCGRTmRNA by ~60% in both diploid and trisomic cells. Overexpression of APP in diploid fibroblasts and HepG2 cells resulted in a decrease inFCGRTand FcRn expression. Our results indicate that the intracellular traffic of IgG is altered in cells with trisomy 21. This study lays the foundation for future investigations into the role of FcRn in the context of DS.
EMT changes actin cortex rheology in a cell-cycle dependent manner
Authors: Hosseini K. , Frenzel A. , Fischer-Friedrich E. 
Published: December 2020

The actin cortex is a key structure for cellular mechanics and cellular migration. Accordingly, cancer cells were shown to change their actin cytoskeleton and their mechanical properties in correlation with different degrees of malignancy and metastatic potential. Epithelial-Mesenchymal transition (EMT) is a cellular transformation associated with cancer progression and malignancy. To date, a detailed study of the effects of EMT on the frequency-dependent viscoelastic mechanics of the actin cortex is still lacking. In this work, we have used an established AFM-based method of cell confinement to quantify the rheology of the actin cortex of human breast, lung and prostate epithelial cells before and after EMT in a frequency range of 0.02 – 2 Hz. Interestingly, we find for all cell lines opposite EMT-induced changes in interphase and mitosis; while the actin cortex softens upon EMT in interphase, the cortex stiffens in mitosis. Our rheological data can be accounted for by a rheological model with a characteristic time scale of slowest relaxation. In conclusion, our study discloses a consistent rheological trend induced by EMT in human cells of diverse tissue origin reflecting major structural changes of the actin cytoskeleton upon EMT.Significance statementThe actin cortex is a key structure for cellular mechanics and cellular migration. Correspondingly, migratory cancer cells were shown to change their mechanical properties to a softer phenotype. EMT is a cellular transformation associated with cancer progression and malignancy. To date, a detailed study of the effects of EMT on the mechanics of the actin cortex is still lacking. In this work, we provide such a study for human breast, lung and prostate epithelial cells in dependence of the cell cycle stage. We observe a softening of the actin cortex in interphase but stiffening in mitosis upon EMT. In conclusion, our study discloses a consistent mechanical trend induced by EMT in human cells of diverse tissue origin.
Neural network aided approximation and parameter inference of stochastic models of gene expression
Authors: Jiang Qingchao , Fu Xiaoming , Yan Shifu , Li Runlai , Du Wenli , Cao Zhixing , Qian Feng , Grima Ramon 
Published: December 2020

AbstractNon-Markov models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis and simulation of these models, as well as the inference of their parameters from data, are fraught with difficulties because the dynamics depends on the system’s history. Here we use an artificial neural network to approximate the time-dependent distributions of non-Markov models by the solutions of much simpler time-inhomogeneous Markov models; the approximation does not increase the dimensionality of the model and simultaneously leads to inference of the kinetic parameters. The training of the neural network uses a relatively small set of noisy measurements generated by experimental data or stochastic simulations of the non-Markov model. We show using a variety of models, where the delays stem from transcriptional processes and feedback control, that the Markov models learnt by the neural network accurately reflect the stochastic dynamics across parameter space.
Decreased autophagy of vascular smooth muscle cells was involved in hyperhomocysteinemia‐induced vascular ageing
Authors: Yan Wenjing , Cao Yan , Zhen Panpan , Ji Dengyu , Chai Jiayin , Xue Ke , Dai Hongyan , Wang Wen 
Published: December 2020

AbstractAgeing and hyperhomocysteinemia (HHcy) are important risk factors for cardiovascular diseases (CVDs). HHcy affects the occurrence of vascular diseases in the elderly. So far, the mechanism of HHcy‐induced vascular ageing remains largely unknown. Autophagy level is significantly reduced in the ageing process, and restoring impaired autophagy to a normal state may be one of the possible ways to extend the expected longevity and lifespan in the future. In this study, we established the HHcy rat model by feeding a 2.5% methionine diet. Small animal ultrasound and the tail‐cuff method indicated that the vascular pulse wave velocity (PWV) and pulse pressure (PP) of HHcy rats were increased significantly compared with the control group. Vascular morphology and structure have been changed in HHcy rats, including lumen dilation, increased collagen fibre deposition and increased p53/p21/p16 expression. In vitro, under the stimulation of homocysteine (500 μmol/L, 24 hours), the rat vascular smooth muscle cells (VSMCs) presented senescence, which was characterized by the increased expression of ageing‐related markers, such as p16, p21 and p53 as well as increased senescence‐associated beta‐galactosidase (SA‐β‐gal) activity. Meanwhile, the autophagy level was decreased both in vivo and in vitro, shown as the increased level of autophagy substrate p62 and the reduced level of autophagy marker LC3 II/I in the thoracic aorta of HHcy rats and in Hcy‐treated VSMCs, respectively. The senescence phenotype of VSMCs was reversed by increased autophagy levels induced by rapamycin. Our findings indicate that decreased autophagy of VSMCs is involved in hyperhomocysteinemia‐induced vascular ageing.
Exploring the influence of stakeholder personality on crisis response evaluations and outcomes
Authors: Brown‐Devlin Natalie , Lim Hayoung Sally , Bouchacourt Lindsay , Devlin Michael B. 
Published: December 2020

AbstractWhile public relations professionals are beginning to utilize psychographic data for more refined audience targeting methods, this study examines how elemental personality traits impact (1) crisis communication outcomes (lessen levels of attributed crisis responsibility, improve individual's reputation and increase positive word‐of‐mouth) and (2) evaluations of crisis response strategies during a paracrisis. This study utilized an experimental design with 368 collegiate participants. Results suggest that several underlying personality traits predict reputation repair‐outcomes regardless of the communication strategy used. For example, findings suggested that stakeholders who rated higher in gentleness and lower in modesty and social boldness reported higher reputational scores pertaining to the offending individual. Yet, other traits, such as prudence, interacted with strategies that prompt the offending individual's preferred crisis communication outcomes.
Acorn flour properties depending on the production method and laboratory baking test results: A review
Authors: Szabłowska Emilia , Tańska Małgorzata 
Published: December 2020

AbstractAcorns, the fruit of the oak, have long been an important source of food in different cultures around the world. Despite their long culinary tradition, they have become under‐appreciated. Due to their high starch content, acorns are mainly used for flour production, and acorn flour is considered as a replacement for cereal flour in a wide range of applications in food production. This study reviewed the published literature concerning acorn flour production and composition as well as the possibility of using acorn flour in the most popular flour‐based products such as bread, cake, and cookies. The study also presents the advantages resulting from acorn flour incorporation to the human diet and acorn flour influence on the quality of bread and pastry products. This review found that acorn flour is characterized by a lack of gluten proteins and a high content of fiber and minerals as well as the presence of polyphenols with antioxidant properties. However, negative impact of its larger amount on the dough rheological features and product physical properties has been emphasized in many studies. The researchers recommend the incorporation of acorn flour up to a level of 15% in formulating composite flour for bread production. However, the literature data indicates that acorn flour substitution for pastry production depends on the product type and ranges from 10 to even 60%. It is also highlighted that the application of acorn flour into gluten‐free products is particularly favorable from a nutritional point of view.
Insights on the use of alternative solvents and technologies to recover bio‐based food pigments
Authors: de Souza Mesquita Leonardo M. , Martins Margarida , Pisani Luciana P. , Ventura Sónia P. M. , de Rosso Veridiana V. 
Published: December 2020

AbstractThis review will discuss, under the Circular Economy and Biorefinery concepts, the performance of the alternative solvents in the downstream process to recover natural pigments in a more sustainable way. Conventionally, pigments marketed on an industrial scale are produced through chemical synthesis by using petroleum derivatives as the main raw material. Also, the current production chain of the synthetic dyes is linear, with no solvent recycling and waste generation. Thus, the most promising processes of extraction and purification of natural pigments and strategies on the polishing of the solvents are here reviewed. In this review, the use of alternative solvents, namely, ionic liquids, eutectic solvents, aqueous solutions of surfactants, and edible oils, for recovering natural pigments was reviewed. Works discussing higher extraction yields and selectivity, while maintaining the stability of the target pigments, were reported. Also, a panorama between Sustainability and Circular Economy prospection was discussed for better comprehension of the main advances in the field. Behind the analysis of the works published so far on the theme, the most important lacunas to overcome in the next years on the field were pointed out and discussed. Also, the future trends and new perspectives to achieve the economic viability and sustainability of the processes using alternative solvents will be scrutinized.
Bacterial spores in spices and dried herbs: The risks for processed food
Authors: Mathot Anne Gabrielle , Postollec Florence , Leguerinel Ivan 
Published: December 2020

AbstractProduction and world consumption of spices are constantly increasing. Although the antimicrobial properties of some spices are well documented, their use in the agri‐food industry is also responsible for microbial contamination and spoilage. Bacterial spores introduced by spices can withstand different preparation processes, particularly thermal treatments, leading to food alterations during storage. This review brings together data from the literature about the prevalence and concentrations of spore‐forming bacteria in all commercially available spices. The sporeformers found in spices belong mainly to the genera Bacillus and Clostridium. Such contaminations are very common and sometimes reach high levels, as in pepper and turmeric. Bacillus licheniformis and Bacillus cereus are the most frequently detected species. Studying the harvesting, processing, and storage procedures for spices provides elements to explain why high prevalence and concentrations are observed. Spices are mostly produced in developing countries on small farms using traditional production methods. Spices become contaminated by bacterial spores in two main ways: by contact with soil during harvesting or drying, as for pepper, or by cross‐contamination during the water‐cooking step, as for turmeric. From these observations, we propose some recommendations. Different methods that can be used to eliminate bacterial spores from spices are presented indicating their efficiency and the limitations of their use.
High prevalence of neurodevelopmental problems in adolescents eligible for bariatric surgery for severe obesity
Authors: Björk Anna , Dahlgren Jovanna , Gronowitz Eva , Henriksson Wessely Fanny , Janson Annika , Engström My , Sjögren Lovisa , Olbers Torsten , Järvholm Kajsa 
Published: December 2020

AbstractAimTo assess the prevalence of neurodevelopmental problems in adolescents with severe obesity and their associations with binge eating and depression.MethodsData were collected at inclusion in a randomised study of bariatric surgery in 48 adolescents (73% girls; mean age 15.7 ± 1.0 years; mean body mass index 42.6 ± 5.2 kg/m2). Parents completed questionnaires assessing their adolescents’ symptoms of attention‐deficit/hyperactivity disorder and autism spectrum disorder and reported earlier diagnoses. Patients answered self‐report questionnaires on binge eating and depressive symptoms.ResultsThe parents of 26/48 adolescents (54%) reported scores above cut‐off for symptoms of the targeted disorders in their adolescents, but only 15% reported a diagnosis, 32% of adolescents reported binge eating, and 20% reported symptoms of clinical depression. No significant associations were found between neurodevelopmental problems and binge eating or depressive symptoms. Only a third of the adolescents reported no problems in either area.ConclusionTwo thirds of adolescents seeking surgical weight loss presented with substantial mental health problems (reported by themselves or their parents). This illustrates the importance of a multi‐professional approach and the need to screen for and treat mental health disorders in adolescents with obesity.
Saving the most lives—A comparison of European triage guidelines in the context of the COVID‐19 pandemic
Authors: Ehni Hans‐Jörg , Wiesing Urban , Ranisch Robert 
Published: December 2020

AbstractIn March 2020, the rapid increase in severe COVID‐19 cases overwhelmed the healthcare systems in several European countries. The capacities for artificial ventilation in intensive care units were too scarce to care for patients with acute respiratory disorder connected to the disease. Several professional associations published COVID‐19 triage recommendations in an extremely short time: in 21 days between March 6 and March 27. In this article, we compare recommendations from five European countries, which combine medical and ethical reflections on this situation in some detail. Our aim is to provide a detailed overview on the ethical elements of the recommendations, the differences between them and their coherence. In more general terms we want to identify shortcomings in regard to a common European response to the current situation.
Assessment of the different skin sensitization potentials of irritants and allergens as single substances and in combination using the KeratinoSens assay
Authors: De Rentiis Anna M. A. , Pink Mario , Verma Nisha , Schmitz‐Spanke Simone 
Published: December 2020

AbstractBackgroundPeople are exposed to mixtures containing allergens and irritants often causing contact dermatitis. Therefore, regulatory authorities require systematic information on the effects of mixtures on the sensitization threshold. In this study a moderate (cinnamal) and a weak (ethylene glycol dimethacrylate) allergen were combined with irritants covering different mechanisms of action (sodium dodecyl sulfate, salicylic acid, and α‐pinene). For a systematic approach, the single substances were initially tested using the KeratinoSens assay. Thereafter, each allergen was combined with noncytotoxic concentrations of the irritants.MethodThe KeratinoSens assay was applied for the single substances according to OECD (Organisation for Economic Co‐operation and Development) Test Guideline 442D. Based on these results, three noncytotoxic concentrations of the irritants were selected and applied simultaneously with 12 concentrations of the allergens to the KeratinoSens cells. Sensitization threshold and cytotoxicity were measured and compared with the individual testing.ResultsThe combinations of allergens and irritants differed from the effects of the single substances and lowered the sensitization threshold. The quantitative approach allowed a clear description of the changes which varied by factors between 1.1 and 10.3.ConclusionsOverall, the allergen was the prominent compound in the mixture and its nature appeared to determine the degree of the response.
Resection rate curves by location along the small intestine provide perspectives on characteristics of Crohn’s disease
Authors: Suzuki Hideyuki , Watanabe Kazuhiro , Kohyama Atsushi , Ohnuma Shinobu , Karasawa Hideaki , Kajiwara Taiki , Kobayashi Minoru , Hatsuzawa Yuuri , Kamei Takashi , Unno Michiaki 
Published: December 2020

AbstractAimCrohn's disease (CD) can affect any part of the gastrointestinal tract; however, the frequency of CD lesions differs by location. This work aimed to examine resection rates by location to clarify locational characteristics of the small intestine in surgical CD cases.MethodThis was a single‐centre retrospective case note review of patients who had undergone resection for CD affecting the small intestine between January 2014 and February 2020. Operative details, including length of the small intestine, location and extent of the resection, identified the pattern of disease. By normalizing these data the resection rate along the length of the intestine was calculated to create resection rate curves.ResultsOne hundred and twenty six surgical cases were identified. The resection rate curves could be divided into two types: exponential and bimodal. For primary surgery, this depended on whether or not surgery was limited to an ileocolic resection. At subsequent surgery, a previous ileocaecal resection influenced the pattern of disease. The peaks of the bimodal curve were located at the proximal and distal ileum.ConclusionCD patients requiring resection of the small intestine can be divided into terminal ileum type (exponential type) and proximal ileum type (bimodal type). In the future this analytical method may help predict the site of any recurrent disease but also provides a new perspective on the disease.
Alpha modulation in younger and older adults during distracted encoding
Authors: Wynn Syanah C. , Nyhus Erika , Jensen Ole 
Published: December 2020

AbstractTo successfully encode information into long‐term memory, we need top‐down control to focus our attention on target stimuli. This attentional focus is achieved by the modulation of sensory neuronal excitability through alpha power. Failure to modulate alpha power and to inhibit distracting information has been reported in older adults during attention and working memory tasks. Given that alpha power during encoding can predict subsequent memory performance, aberrant oscillatory modulations might play a role in age‐related memory deficits. However, it is unknown whether there are age‐related differences in memory performance or alpha modulation when encoding targets with distraction. Here we show that both older and younger adults are able to encode targets paired with distractors and that the level of alpha power modulation during encoding predicted recognition success. Even though older adults showed signs of higher distractibility, this did not harm their episodic memory for target information. Also, we demonstrate that older adults only modulated alpha power during high distraction, both by enhancing target processing and inhibiting distractor processing. These results indicate that both younger and older adults are able to employ the same inhibitory control mechanisms successfully, but that older adults fail to call upon these when distraction is minimal. The findings of this study give us more insight into the mechanisms involved in memory encoding across the lifespan.