bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell encapsulation in alginate-based microgels using droplet microfluidics; a review on gelation methods and applications
Authors: Mohajeri Mohammad , Eskandari Mahnaz , Ghazali Zahra Sadat , Ghazali Hanieh Sadat 
Published: January 2022

Abstract
Cell encapsulation within the microspheres using a semi-permeable polymer allows the two-way transfer of molecules such as oxygen, nutrients, and growth factors. The main advantages of cell encapsulation technology include controlling the problems involved in transplanting rejection in tissue engineering applications and reducing the long-term need for immunosuppressive drugs following organ transplantation to eliminate the side effects. Cell-laden microgels can also be used in 3D cell cultures, wound healing, and cancerous clusters for drug testing. Since cell encapsulation is used for different purposes, several techniques have been developed to encapsulate cells. Droplet-based microfluidics is one of the most valuable techniques in cell encapsulating. This study aimed to review the geometries and the mechanisms proposed in microfluidic systems to precisely control cell-laden microgels production with different biopolymers. We also focused on alginate gelation techniques due to their essential role in cell encapsulation applications. Finally, some applications of these microgels and researches will be explored.
Unravelling the bending stability of flexible quantum-dot light-emitting diodes
Authors: Wang Rujing , Yuan Qilin , Kang Zhihui , Wang Rong , Zhang Dandan , Ji Wenyu 
Published: January 2022

Abstract
The bending stability is still the central obstacle to the practical applications of flexible quantum-dot light-emitting diodes (QLED). Here, we examine the influence of every functional layer, including electrodes, charge injection/transport layers, and emission layer, on the photoelectrical properties of the QLEDs during the bending fatigue test. It is demonstrated that the bottom substrate and top metal electrode play a critical role in determining the bending stability of flexible QLEDs. The bending stability of the QLED can be improved obviously by controlling the elastic modulus and surface roughness of the substrate with a poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) modifying layer inserted between PET/ITO/Ag/ITO and ZnO electron-transport layer. The PEDOT:PSS layer not only reduces the surface roughness, but also causes the neutral mechanical plane of the PET/ITO/Ag/ITO multilayer to move towards the surface of the substrate. The twofold effect of this PEDOT:PSS modifying layer improves the bending stability of the device. Moreover, the device efficiency is also enhanced from 17.9 to 20.4 cd A−1 with the insertion of PEDOT:PSS layer.
A spiking neuron implemented in VLSI
Authors: Stoliar P , Akita I , Schneegans O , Hioki M , Rozenberg M J 
Published: January 2022

Abstract
A VLSI implementation of a Silicon-Controlled Rectifier (SCR)-based Neuron that has the functionality of the leaky-integrate and fire model (LIF) of spiking neurons is introduced. The silicon-controlled rectifier is not straightforward to efficiently migrate to VLSI. Therefore, we propose a MOS transistor-based circuit that provides the same functionality as the SCR. The results of this work are based on Spice simulation using open libraries and on VLSI layout and post layout simulations for a 65 nm CMOS process.
How sticky are our proteins? Quantifying hydrophobicity of the human proteome
Authors: van Gils Juami Hermine Mariama , Gogishvili Dea , van Eck Jan , Bouwmeester Robbin , van Dijk Erik , Abeln Sanne 
Published: January 2022

Abstract

Summary
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some ‘sticky’ hydrophobic residues to the solvent. These residues can play an important functional role, e.g. in protein–protein and membrane interactions. Here, we first investigate how hydrophobic protein surfaces are by providing three measures for surface hydrophobicity: the total hydrophobic surface area, the relative hydrophobic surface area and—using our MolPatch method—the largest hydrophobic patch. Secondly, we analyze how difficult it is to predict these measures from sequence: by adapting solvent accessibility predictions from NetSurfP2.0, we obtain well-performing prediction methods for the THSA and RHSA, while predicting LHP is more challenging. Finally, we analyze implications of exposed hydrophobic surfaces: we show that hydrophobic proteins typically have low expression, suggesting cells avoid an overabundance of sticky proteins.

Availability and implementation
The data underlying this article are available in GitHub at https://github.com/ibivu/hydrophobic_patches.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Struct-f4: a Rcpp package for ancestry profile and population structure inference from f4-statistics
Authors: Librado Pablo , Orlando Ludovic 
Published: January 2022

Abstract

Summary
Visualization and inference of population structure is increasingly important for fundamental and applied research. Here, we present Struct-f4, providing automated solutions to characterize and summarize the genetic ancestry profile of individuals, assess their genetic affinities, identify admixture sources and quantify admixture levels.

Availability and implementation
Struct-f4 is written in Rcpp and relies on f4-statistics and Markov Chain Monte Carlo (MCMC) optimization. It is freely available under GNU General Public License in Bitbucket (https://bitbucket.org/plibradosanz/structf4/).

Supplementary information
Supplementary data are available at Bioinformatics online.
The Impact of Internship Experience on Schooling and Labour Market Outcomes
Authors: Neyt Brecht , Verhaest Dieter , Navarini Lorenzo , Baert Stijn 
Published: January 2022

Abstract
We examine the impact of internship experience during secondary education on students’ schooling and early labour market outcomes by analysing unique, longitudinal data from Belgium. To control for unobservable differences between students with and students without internship experience, we estimate a dynamic discrete choice model. In line with literature on vocational education, we find that internship experience has a positive effect on one’s employment chances up to 5 years after graduation. This positive effect is mainly explained by a positive direct employment effect. Although we also find a positive indirect employment effect through a higher chance to obtain a secondary education qualification, this is largely compensated by negative indirect effects through lower tertiary education attainment. (JEL codes: I21, I26, J21, and J24)
Farewell from the CKJ Editor-in-Chief: key kidney topics from 2014 to 2021
Authors: Ortiz Alberto , Vinck Caroline 
Published: January 2022

ABSTRACT
The year 2021 was the last full year of Alberto Ortiz’s editorship at Clinical Kidney Journal (CKJ). On May 2022, Maria José Soler will start her term as the Editor-in-Chief. Over these years, CKJ obtained its first journal impact factor and has consolidated its position among the top journals in the field, consistently ranking among the top 25% (first quartile) journals in Urology and Nephrology. The 2020 journal impact factor rose to 4.45, becoming the top open access journal in Nephrology and the ninth ranked Nephrology journal overall. We now review the recent history of the journal and the most highly cited topics which include the epidemiology of kidney disease, chronic kidney disease topics, such as the assessment and treatment of chronic kidney disease, onconephrology, cardionephrology, glomerular disease, transplantation and coronavirus disease 2019 (COVID-19).
Cliques in geometric inhomogeneous random graphs
Authors: Michielan Riccardo , Stegehuis Clara 
Published: January 2022

Abstract
Many real-world networks were found to be highly clustered and contain a large amount of small cliques. We here investigate the number of cliques of any size $k$ contained in a geometric inhomogeneous random graph: a scale-free network model containing geometry. The interplay between scale-freeness and geometry ensures that connections are likely to form between either high-degree vertices, or between close by vertices. At the same time, it is rare for a vertex to have a high degree, and most vertices are not close to one another. This trade-off makes cliques more likely to appear between specific vertices. In this article, we formalize this trade-off and prove that there exists a typical type of clique in terms of the degrees and the positions of the vertices that span the clique. Moreover, we show that the asymptotic number of cliques as well as the typical clique type undergoes a phase transition, in which only $k$ and the degree-exponent $\tau$ are involved. Interestingly, this phase transition shows that for small values of $\tau$, the underlying geometry of the model is irrelevant: the number of cliques scales the same as in a non-geometric network model.
An empirical comparison of connectivity-based distances on a graph and their computational scalability
Authors: Miasnikof Pierre , Shestopaloff Alexander Y , Pitsoulis Leonidas , Ponomarenko Alexander 
Published: January 2022

Abstract
In this study, we compare distance measures with respect to their ability to capture vertex community structure and the scalability of their computation. Our goal is to find a distance measure which can be used in an aggregate pairwise minimization clustering scheme. The minimization should lead to subsets of vertices with high induced subgraph density. Our definition of distance is rooted in the notion that vertices sharing more connections are closer to each other than vertices which share fewer connections. This definition differs from that of the geodesic distance typically used in graphs. It is based on neighbourhood overlap, not shortest path. We compare four distance measures from the literature and evaluate their accuracy in reflecting intra-cluster density, when aggregated (averaged) at the cluster level. Our tests are conducted on synthetic graphs, where clusters and intra-cluster densities are known in advance. We find that amplified commute, Otsuka–Ochiai and Jaccard distances display a consistent inverse relation to intra-cluster density. We also conclude that the computation of amplified commute distance does not scale as well to large graphs as that of the other two distances.
A pragmatic lab-based tool for risk assessment in cardiac critical care: data from the Critical Care Cardiology Trials Network (CCCTN) Registry
Authors: Patel Siddharth M , Jentzer Jacob C , Alviar Carlos L , Baird-Zars Vivian M , Barsness Gregory W , Berg David D , Bohula Erin A , Daniels Lori B , DeFilippis Andrew P , Keeley Ellen C , Kontos Michael C , Lawler Patrick R , Miller P Elliott , Park Jeong-Gun , Roswell Robert O , Solomon Michael A , van Diepen Sean , Katz Jason N , Morrow David A ,   the CCCTN Investigators
Published: January 2022

Abstract

Aims
Contemporary cardiac intensive care unit (CICU) outcomes remain highly heterogeneous. As such, a risk-stratification tool using readily available lab data at time of CICU admission may help inform clinical decision-making.

Methods and results
The primary derivation cohort included 4352 consecutive CICU admissions across 25 tertiary care CICUs included in the Critical Care Cardiology Trials Network (CCCTN) Registry. Candidate lab indicators were assessed using multivariable logistic regression. An integer risk score incorporating the top independent lab indicators associated with in-hospital mortality was developed. External validation was performed in a separate CICU cohort of 9716 patients from the Mayo Clinic (Rochester, MN, USA). On multivariable analysis, lower pH [odds ratio (OR) 1.96, 95% confidence interval (CI) 1.72–2.24], higher lactate (OR 1.40, 95% CI 1.22–1.62), lower estimated glomerular filtration rate (OR 1.26, 95% CI 1.10–1.45), and lower platelets (OR 1.18, 95% CI 1.05–1.32) were the top four independent lab indicators associated with higher in-hospital mortality. Incorporated into the CCCTN Lab-Based Risk Score, these four lab indicators identified a 20-fold gradient in mortality risk with very good discrimination (C-index 0.82, 95% CI 0.80–0.84) in the derivation cohort. Validation of the risk score in a separate cohort of 3888 patients from the Registry demonstrated good performance (C-index of 0.82; 95% CI 0.80–0.84). Performance remained consistent in the external validation cohort (C-index 0.79, 95% CI 0.77–0.80). Calibration was very good in both validation cohorts (r = 0.99).

Conclusion
A simple integer risk score utilizing readily available lab indicators at time of CICU admission may accurately stratify in-hospital mortality risk.
The role of cardiovascular magnetic resonance in the evaluation of acute myocarditis and inflammatory cardiomyopathies in clinical practice — a comprehensive review
Authors: Ismail Tevfik F , Hua Alina , Plein Sven , D’Cruz David P , Fernando Michelle M A , Friedrich Matthias G , Zellweger Michael J , Giorgetti Assuero , Caobelli Federico , Haaf Philip 
Published: January 2022

AbstractInflammatory cardiomyopathy (I-CMP) is defined as myocarditis in association with cardiac dysfunction and/or ventricular remodelling. It is characterized by inflammatory cell infiltration into the myocardium and has heterogeneous infectious and non-infectious aetiologies. A complex interplay of genetic, autoimmune, and environmental factors contributes to the substantial risk of deteriorating cardiac function, acute heart failure, and arrhythmia as well as chronic dilated cardiomyopathy and its sequelae. Multi-parametric cardiovascular magnetic resonance (CMR) imaging is sensitive to many tissue changes that occur during myocardial inflammation, regardless of its aetiology. In this review, we summarize the various aetiologies of I-CMP and illustrate how CMR contributes to non-invasive diagnosis.
Coronary protection for the small left coronary sinus during transcatheter aortic valve replacement: a case report
Authors: Yang Chen , Song Guangyuan , Niu Guannan , Wu Yongjian 
Published: January 2022

Abstract

Background
Coronary obstruction (CO) is an infrequent but life-threatening complication during transcatheter aortic valve replacement (TAVR).

Case summary
We report the case of a patient who accepted TAVR with high anatomical risks of CO due to the small congenital left coronary sinus, which was treated with preliminary coronary protection. This case highlighted the importance of computed tomography angiography (CTA) evaluation, 3D-printing stimulation, predilation as a reference sign, and pre-emptive chimney stenting technology to successfully anticipate and prevent CO during TAVR. At the 3rd month follow-up, CTA evaluation and 3D-printing simulation identified the chimney stenting of the left main coronary arterial patency.

Discussion
A ‘four-step assessment’ method also proposes a new clinical procedure on how to perform TAVR in patients with high risks of CO.
The Genome of the Poecilogonous Annelid Streblospio benedicti
Authors: Zakas Christina , Harry Nathan D , Scholl Elizabeth H , Rockman Matthew V 
Published: January 2022

Abstract
Streblospio benedicti is a common marine annelid that has become an important model for developmental evolution. It is the only known example of poecilogony (where two distinct developmental modes occur within a single species) that is due to a heritable difference in egg size. The dimorphic developmental programs and life-histories exhibited in this species depend on differences within the genome, making it an optimal model for understanding the genomic basis of developmental divergence. Studies using S. benedicti have begun to uncover the genetic and genomic principles that underlie developmental uncoupling, but until now they have been limited by the lack of availability of genomic tools. Here, we present an annotated chromosomal-level genome assembly of S. benedicti generated from a combination of Illumina reads, Nanopore long reads, Chicago and Hi-C chromatin interaction sequencing, and a genetic map from experimental crosses. At 701.4 Mb, the S. benedicti genome is the largest annelid genome to date that has been assembled to chromosomal scaffolds. The complete genome of S. benedicti is valuable for functional genomic analyses of development and evolution, as well as phylogenetic comparison within the annelida and the Lophotrochozoa. Despite having two developmental modes, there is no evidence of genome duplication or substantial gene number expansions. Instead, lineage-specific repeats account for much of the expansion of this genome compared with other annelids.
The Right to a Fair Online Hearing
Authors: Kamber Krešimir 
Published: January 2022

Abstract
With the outbreak of the Covid-19 pandemic, the courts almost invariably (although to different degrees) started closing doors to physical presence and a new interest in remote forms of the administration of justice—notably online hearings—has emerged from the margins of legal research and practice. This article focuses on online hearings as the most critical aspect of the remote administration of justice, which still remains, theoretically and empirically, a largely unexplored area of legal process. It discusses the conceptual problems of online hearings from the perspective of European human rights law, notably Article 6 (the right to a fair trial) of the European Convention on Human Rights. On the basis of this assessment, the article identifies the limits to the use of online hearings flowing from the perspective of the right to a fair trial. It also cautions against any injudicious attempts to turn the pandemic-related extraordinary mode of functioning of court hearings into a new ordinary state of affairs and proposes ways in which the associated risks could be averted.
The protein level of the tumour-promoting factor SET is regulated by cell density
Authors: Kohyanagi Naoki , Kitamura Nao , Tanaka Keiko , Mizuno Takuya , Fujiwara Nobuyuki , Ohama Takashi , Sato Koichi 
Published: January 2022

Abstract
SET/I2PP2A is a multifunctional protein that acts as an intrinsic inhibitor of the tumour suppressor protein phosphatase 2A and as a histone chaperone. Increased SET levels have been observed in various cancers; however, the underlying molecular mechanisms remain unclear. In this study, we found that SET protein accumulates with the increasing density of cultured cells. This phenomenon was observed not only in cancer cell lines but also in non-cancer cell lines. The mRNA levels of SET were not affected by the cell density. Proteasome inhibition decreased SET levels, whereas autophagy inhibition led to SET accumulation, indicating the involvement of autophagy. The mRNA and protein expression of SETBP1, which stabilizes the SET protein, increased with cell density. The decrease in SET level due to the loss of SETBP1 was more pronounced in wild-type cells than that in autophagy-deficient cells. These results have revealed a mechanism underlying the regulation of SET level, wherein increased cell density induces SETBP1 expression and protects SET from autophagy.
Straining the Spaghetti Bowl: Re-Evaluating the Regulation of Preferential Rules of Origin
Authors: Delev Christian 
Published: January 2022

ABSTRACT
Preferential rules of origin (PROOs) are a hallmark of the modern Regional Trade Agreement network. However, the ever-rising use of PROOs has revealed their dual economic function: to prevent trade deflection from occurring, and to export domestic State protectionism to the regional level. This paper challenges existing scholarship and reassesses the WTO disciplines applicable to PROOs. Using the United States-Mexico-Canada Agreement as a case-study, it examines the ways in which PROOs have obstructed trade liberalization at the regional level in favour of embedding protectionism in certain sectors. The disciplines under Article III:4 GATT, Annex II of the Agreement on Rules of Origin, and the Trade Facilitation Agreement are then shown to limit Members’ discretion in adopting PROOs. Finally, the internal and external conditions of Article XXIV GATT further restrain the extent to which Members may lawfully export their domestic protectionism through Regional Trade Agreements. Crucially, violations of the restraints under Article XXIV GATT are unlikely to be justified based on Article XX(d) GATT.
Mechanisms of coexistence in a diverse Neotropical mammalian carnivore community
Authors: Zuercher Gerald L , Owen Robert D , Torres Julio , Gipson Philip S 
Published: January 2022

AbstractMammalian carnivore diversity within the Reserva Natural del Bosque Mbaracayú in eastern Paraguay is represented by five families (Canidae, Mephitidae, Mustelidae, Procyonidae, and Felidae) and includes large-bodied, apex predators, several omnivores, and numerous mesocarnivores. The competitive exclusion principle argues that sustained spatial and temporal coexistence of two or more species with identical ecological requirements is unsustainable. The Reserve is a mosaic of habitats that has become isolated due to extensive deforestation of the surrounding Upper Paraná Atlantic Forest. Nevertheless, it is remarkable in that 16 mammalian carnivore species are documented as coexisting within the Reserve. We sought to determine the extent to which this diverse community is mitigating competition through the partitioning of available niche space by assessing dietary ecology of mammalian carnivores present, including diet breadths and dietary overlap, and by examining spatial patterns within the reserve. Feces were collected from all 16 mammalian carnivore species from seven areas within the reserve and specific identifications were confirmed by molecular analyses. Diet breadth, B^, standardized diet breadth, B^A, and Pianka’s Index for dietary overlap, O^, were calculated. A Chi-square goodness-of-fit test was performed to test for randomness of samples associated with survey areas. Diet analyses indicated a spectrum from dietary generalists to specialists. Species segregated into six dietary guilds, defined as groups of species with O^ &gt; 0.5. Four guilds included only one species each (Neotropical otter, crab-eating fox, jaguar, and puma). The low dietary overlap between jaguar and puma contrasts with studies conducted elsewhere. One guild consisted of four highly omnivorous species (maned wolf, Molina’s hog-nosed skunk, crab-eating raccoon, and South American coati). The sixth guild included eight species which mostly consumed small vertebrates, primarily mammals as well as birds and reptiles (bush dog, two mustelines, five small felids). The mustelines (tayra and lesser grison) had extremely high dietary overlap. Although they did not segregate spatially, they are known to occupy distinct niches in vertically stratified forests. The five small felids also showed extremely high dietary overlap. Three of them were found to segregate spatially within the Reserve and two did not, although one (jaguarundi) is known to segregate temporally, being more active diurnally. The exceptionally rich community of mammalian carnivore species at the Reserva Natural del Bosque Mbaracayú appeared to avoid unsustainable competition by a variety of mechanisms, some utilizing different food items, or, in the case of high dietary overlap, utilizing spatial or temporal resources differently.