bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trophic flexibility of marine diplonemids - switching from osmotrophy to bacterivory
Authors: Prokopchuk Galina , Korytář Tomáš , Juricová Valéria , Majstorović Jovana , Horák Aleš , Šimek Karel , Lukeš Julius 
Published: January 2022

Abstract
Diplonemids are one of the most abundant groups of heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. So far, only few species have been introduced into a culture, allowing basic studies of diplonemid genetics, morphology, ultrastructure, metabolism, as well as endosymbionts. However, it remains unclear whether these heterotrophic flagellates are parasitic or free-living and what are their predominant dietary patterns and preferred food items. Here we show that cultured diplonemids, maintained in an organic-rich medium as osmotrophs, can gradually switch to bacterivory as a sole food resource, supporting positive growth of their population, even when fed with a low biovolume of bacteria. We further observed remarkable differences in species-specific feeding patterns, size-selective grazing preferences, and distinct feeding strategies. Diplonemids can discriminate between low-quality food items and inedible particles, such as latex beads, even after their ingestion, by discharging them in the form of large waste vacuoles. We also detected digestion-related endogenous autofluorescence emitted by lysosomes and the activity of a melanin-like material. We present the first evidence that these omnipresent protists possess an opportunistic lifestyle that provides a considerable advantage in the generally food resource-limited marine environments.
Intra-crystalline mesoporous zeolite encapsulation-derived thermally robust metal nanocatalyst in deep oxidation of light alkanes
Authors: Peng Honggen , Dong Tao , Yang Shenyou , Chen Hao , Yang Zhenzhen , Liu Wenming , He Chi , Wu Peng , Tian Jinshu , Peng Yue , Chu Xuefeng , Wu Daishe , An Taicheng , Wang Yong , Dai Sheng 
Published: January 2022

AbstractZeolite-confined metal nanoparticles (NPs) have attracted much attention owing to their superior sintering resistance and broad applications for thermal and environmental catalytic reactions. However, the pore size of the conventional zeolites is usually below 2 nm, and reactants are easily blocked to access the active sites. Herein, a facile in situ mesoporogen-free strategy is developed to design and synthesize palladium (Pd) NPs enveloped in a single-crystalline zeolite (silicalite-1, S-1) with intra-mesopores (termed Pd@IM-S-1). Pd@IM-S-1 exhibited remarkable light alkanes deep oxidation performances, and it should be attributed to the confinement and guarding effect of the zeolite shell and the improvement in mass-transfer efficiency and active metal sites accessibility. The Pd−PdO interfaces as a new active site can provide active oxygen species to the first C−H cleavage of light alkanes. This work exemplifies a promising strategy to design other high-performance intra-crystalline mesoporous zeolite-confined metal/metal oxide catalysts for high-temperature industrial thermal catalysis.
Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome
Authors: Dutrow Emily V. , Emera Deena , Yim Kristina , Uebbing Severin , Kocher Acadia A. , Krenzer Martina , Nottoli Timothy , Burkhardt Daniel B. , Krishnaswamy Smita , Louvi Angeliki , Noonan James P. 
Published: January 2022

AbstractThe evolution of uniquely human traits likely entailed changes in developmental gene regulation. Human Accelerated Regions (HARs), which include transcriptional enhancers harboring a significant excess of human-specific sequence changes, are leading candidates for driving gene regulatory modifications in human development. However, insight into whether HARs alter the level, distribution, and timing of endogenous gene expression remains limited. We examined the role of the HARHACNS1(HAR2) in human evolution by interrogating its molecular functions in a genetically humanized mouse model. We find thatHACNS1maintains its human-specific enhancer activity in the mouse embryo and modifies expression ofGbx2, which encodes a transcription factor, during limb development. Using single-cell RNA-sequencing, we demonstrate thatGbx2is upregulated in the limb chondrogenic mesenchyme ofHACNS1homozygous embryos, supporting thatHACNS1alters gene expression in cell types involved in skeletal patterning. Our findings illustrate that humanized mouse models provide mechanistic insight into how HARs modified gene expression in human evolution.
Deciphering the mechanism of processive ssDNA digestion by the Dna2-RPA ensemble
Authors: Shen Jiangchuan , Zhao Yiling , Pham Nhung Tuyet , Li Yuxi , Zhang Yixiang , Trinidad Jonathan , Ira Grzegorz , Qi Zhi , Niu Hengyao 
Published: January 2022

AbstractSingle-stranded DNA (ssDNA) commonly occurs as intermediates in DNA metabolic pathways. The ssDNA binding protein, RPA, not only protects the integrity of ssDNA, but also directs the downstream factor that signals or repairs the ssDNA intermediate. However, it remains unclear how these enzymes/factors outcompete RPA to access ssDNA. Using the budding yeast Saccharomyces cerevisiae as a model system, we find that Dna2 — a key nuclease in DNA replication and repair — employs a bimodal interface to act with RPA both in cis and in trans. The cis-activity makes RPA a processive unit for Dna2-catalyzed ssDNA digestion, where RPA delivers its bound ssDNA to Dna2. On the other hand, activity in trans is mediated by an acidic patch on Dna2, which enables it to function with a sub-optimal amount of RPA, or to overcome DNA secondary structures. The trans-activity mode is not required for cell viability, but is necessary for effective double strand break (DSB) repair.
Bridging pico-to-nanonewtons with a ratiometric force probe for monitoring nanoscale polymer physics before damage
Authors: Kotani Ryota , Yokoyama Soichi , Nobusue Shunpei , Yamaguchi Shigehiro , Osuka Atsuhiro , Yabu Hiroshi , Saito Shohei 
Published: January 2022

AbstractUnderstanding the transmission of nanoscale forces in the pico-to-nanonewton range is important in polymer physics. While physical approaches have limitations in analyzing the local force distribution in condensed environments, chemical analysis using force probes is promising. However, there are stringent requirements for probing the local forces generated before structural damage. The magnitude of those forces corresponds to the range below covalent bond scission (from 200 pN to several nN) and above thermal fluctuation (several pN). Here, we report a conformationally flexible dual-fluorescence force probe with a theoretically estimated threshold of approximately 100 pN. This probe enables ratiometric analysis of the distribution of local forces in a stretched polymer chain network. Without changing the intrinsic properties of the polymer, the force distribution was reversibly monitored in real time. Chemical control of the probe location demonstrated that the local stress concentration is twice as biased at crosslinkers than at main chains, particularly in a strain-hardening region. Due to the high sensitivity, the percentage of the stressed force probes was estimated to be more than 1000 times higher than the activation rate of a conventional mechanophore.
Mechanically robust supramolecular polymer co-assemblies
Authors: Sautaux Julien , Marx Franziska , Gunkel Ilja , Weder Christoph , Schrettl Stephen 
Published: January 2022

AbstractSupramolecular polymers are formed through non-covalent, directional interactions between monomeric building blocks. The assembly of these materials is reversible, which enables functions such as healing, repair, or recycling. However, supramolecular polymers generally fail to match the mechanical properties of conventional commodity plastics. Here we demonstrate how strong, stiff, tough, and healable materials can be accessed through the combination of two metallosupramolecular polymers with complementary mechanical properties that feature the same metal-ligand complex as binding motif. Co-assembly yields materials with micro-phase separated hard and soft domains and the mechanical properties can be tailored by simply varying the ratio of the two constituents. On account of toughening and physical cross-linking effects, this approach affords materials that display higher strength, toughness, or failure strain than either metallosupramolecular polymer alone. The possibility to combine supramolecular building blocks in any ratio further permits access to compositionally graded objects with a spatially modulated mechanical behavior.
53BP1 regulates heterochromatin through liquid phase separation
Authors: Zhang Lei , Geng Xinran , Wang Fangfang , Tang Jinshan , Ichida Yu , Sharma Arishya , Jin Sora , Chen Mingyue , Tang Mingliang , Pozo Franklin Mayca , Wang Wenxiu , Wang Janet , Wozniak Michal , Guo Xiaoxia , Miyagi Masaru , Jin Fulai , Xu Yongjie , Yao Xinsheng , Zhang Youwei 
Published: January 2022

AbstractHuman 53BP1 is primarily known as a key player in regulating DNA double strand break (DSB) repair choice; however, its involvement in other biological process is less well understood. Here, we report a previously uncharacterized function of 53BP1 at heterochromatin, where it undergoes liquid-liquid phase separation (LLPS) with the heterochromatin protein HP1α in a mutually dependent manner. Deletion of 53BP1 results in a reduction in heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNA. We identify domains and residues of 53BP1 required for its LLPS, which overlap with, but are distinct from, those involved in DSB repair. Further, 53BP1 mutants deficient in DSB repair, but proficient in LLPS, rescue heterochromatin de-repression and protect cells from stress-induced DNA damage and senescence. Our study suggests that in addition to DSB repair modulation, 53BP1 contributes to the maintenance of heterochromatin integrity and genome stability through LLPS.
Solution-processable, soft, self-adhesive, and conductive polymer composites for soft electronics
Authors: Tan Peng , Wang Haifei , Xiao Furui , Lu Xi , Shang Wenhui , Deng Xiaobo , Song Huafeng , Xu Ziyao , Cao Junfeng , Gan Tiansheng , Wang Ben , Zhou Xuechang 
Published: January 2022

AbstractSoft electronics are rising electronic technologies towards applications spanning from healthcare monitoring to medical implants. However, poor adhesion strength and significant mechanical mismatches inevitably cause the interface failure of devices. Herein we report a self-adhesive conductive polymer that possesses low modulus (56.1-401.9 kPa), high stretchability (700%), high interfacial adhesion (lap-shear strength >1.2 MPa), and high conductivity (1-37 S/cm). The self-adhesive conductive polymer is fabricated by doping the poly(3,4-ethylenedioxythiophene): poly(styrene sulfonate) composite with a supramolecular solvent (β-cyclodextrin and citric acid). We demonstrated the solution process-based fabrication of self-adhesive conductive polymer-based electrodes for various soft devices, including alternating current electroluminescent devices, electromyography monitoring, and an integrated system for the visualization of electromyography signals during muscle training with an array of alternating current electroluminescent devices. The self-adhesive conductive polymer-based electronics show promising features to further develop wearable and comfortable bioelectronic devices with the physiological electric signals of the human body readable and displayable during daily activities.
Mid-infrared emissivity of partially dehydrated asteroid (162173) Ryugu shows strong signs of aqueous alteration
Authors: Hamm M. , Grott M. , Senshu H. , Knollenberg J. , de Wiljes J. , Hamilton V. E. , Scholten F. , Matz K. D. , Bates H. , Maturilli A. , Shimaki Y. , Sakatani N. , Neumann W. , Okada T. , Preusker F. , Elgner S. , Helbert J. , Kührt E. , Ho T.-M. , Tanaka S. , Jaumann R. , Sugita S. 
Published: January 2022

AbstractThe near-Earth asteroid (162173) Ryugu, the target of Hayabusa2 space mission, was observed via both orbiter and the lander instruments. The infrared radiometer on the MASCOT lander (MARA) is the only instrument providing spectrally resolved mid-infrared (MIR) data, which is crucial for establishing a link between the asteroid material and meteorites found on Earth. Earlier studies revealed that the single boulder investigated by the lander belongs to the most common type found on Ryugu. Here we show the spectral variation of Ryugu’s emissivity using the complete set of in-situ MIR data and compare it to those of various carbonaceous chondritic meteorites, revealing similarities to the most aqueously altered ones, as well as to asteroid (101955) Bennu. The results show that Ryugu experienced strong aqueous alteration prior to any dehydration.
Evidence that the Ser192Tyr/Arg402Gln in cis Tyrosinase gene haplotype is a disease-causing allele in oculocutaneous albinism type 1B (OCA1B)
Authors: Lin Siying , Sanchez-Bretaño Aida , Leslie Joseph S. , Williams Katie B. , Lee Helena , Thomas N. Simon , Callaway Jonathan , Deline James , Ratnayaka J. Arjuna , Baralle Diana , Schmitt Melanie A. , Norman Chelsea S. , Hammond Sheri , Harlalka Gaurav V. , Ennis Sarah , Cross Harold E. , Wenger Olivia , Crosby Andrew H. , Baple Emma L. , Self Jay E. 
Published: January 2022

AbstractOculocutaneous albinism type 1 (OCA1) is caused by pathogenic variants in theTYR(tyrosinase) gene which encodes the critical and rate-limiting enzyme in melanin synthesis. It is the most common OCA subtype found in Caucasians, accounting for ~50% of cases worldwide. The apparent ‘missing heritability’ in OCA is well described, with ~25–30% of clinically diagnosed individuals lacking two clearly pathogenic variants. Here we undertook empowered genetic studies in an extensive multigenerational Amish family, alongside a review of previously published literature, a retrospective analysis of in-house datasets, and tyrosinase activity studies. Together this provides irrefutable evidence of the pathogenicity of two commonTYRvariants, p.(Ser192Tyr) and p.(Arg402Gln) when inherited incisalongside a pathogenicTYRvariant intrans. We also show that homozygosity for the p.(Ser192Tyr)/p.(Arg402Gln)TYRhaplotype results in a very mild, but fully penetrant, albinism phenotype. Together these data underscore the importance of including theTYRp.(Ser192Tyr)/p.(Arg402Gln) incishaplotype as a pathogenic allele causative of OCA, which would likely increase molecular diagnoses in this missing heritability albinism cohort by 25–50%.
A 6-mRNA host response classifier in whole blood predicts outcomes in COVID-19 and other acute viral infections
Authors: Buturovic Ljubomir , Zheng Hong , Tang Benjamin , Lai Kevin , Kuan Win Sen , Gillett Mark , Santram Rahul , Shojaei Maryam , Almansa Raquel , Nieto Jose Ángel , Muñoz Sonsoles , Herrero Carmen , Antonakos Nikolaos , Koufargyris Panayiotis , Kontogiorgi Marina , Damoraki Georgia , Liesenfeld Oliver , Wacker James , Midic Uros , Luethy Roland , Rawling David , Remmel Melissa , Coyle Sabrina , Liu Yiran E. , Rao Aditya M. , Dermadi Denis , Toh Jiaying , Jones Lara Murphy , Donato Michele , Khatri Purvesh , Giamarellos-Bourboulis Evangelos J. , Sweeney Timothy E. 
Published: January 2022

AbstractPredicting the severity of COVID-19 remains an unmet medical need. Our objective was to develop a blood-based host-gene-expression classifier for the severity of viral infections and validate it in independent data, including COVID-19. We developed a logistic regression-based classifier for the severity of viral infections and validated it in multiple viral infection settings including COVID-19. We used training data (N = 705) from 21 retrospective transcriptomic clinical studies of influenza and other viral illnesses looking at a preselected panel of host immune response messenger RNAs. We selected 6 host RNAs and trained logistic regression classifier with a cross-validation area under curve of 0.90 for predicting 30-day mortality in viral illnesses. Next, in 1417 samples across 21 independent retrospective cohorts the locked 6-RNA classifier had an area under curve of 0.94 for discriminating patients with severe vs. non-severe infection. Next, in independent cohorts of prospectively (N = 97) and retrospectively (N = 100) enrolled patients with confirmed COVID-19, the classifier had an area under curve of 0.89 and 0.87, respectively, for identifying patients with severe respiratory failure or 30-day mortality. Finally, we developed a loop-mediated isothermal gene expression assay for the 6-messenger-RNA panel to facilitate implementation as a rapid assay. With further study, the classifier could assist in the risk assessment of COVID-19 and other acute viral infections patients to determine severity and level of care, thereby improving patient management and reducing healthcare burden.
Improving the anti-ageing activity of coenzyme Q10 through protransfersome-loaded emulgel
Authors: Ayunin Qurrota , Miatmoko Andang , Soeratri Widji , Erawati Tristiana , Susanto Joni , Legowo Djoko 
Published: January 2022

AbstractCoenzyme Q10 (CoQ10) is a naturally produced organic molecule which acts as an antioxidant agent, including in skin anti-ageing, and plays a major role in the social determinants of health. However, its level in the body will decrease during ageing. Therefore, an external supplement is required to repair damaged skin, especially the skin dermis layer. This study aims to evaluate the use of a protransfersomal emulgel to improve the skin delivery and stability of CoQ10 which demonstrates low water solubility, poor permeability and instability. CoQ10 was initially dissolved in oleic acid at a weight ratio of 1:56. Protransfersome was then loaded with CoQ10 (Protransf-CoQ10) and prepared using a composition of L-α-Phosphatidylcholine and Tween 80 at a molar ratio of 85:15. The Protransf-CoQ10 was dispersed in an emulgel base consisting of Tween 80 and Span 80 to produce Protransf-CoQ10 emulgel. The in vivo studies of anti-aging activity and irritability were further evaluated by applying daily 200 mg of emulgels twice a day to a 4 cm2 section on the back of a UV-ray aging-induced male Balb/c mouse 20 min before irradiation. The results showed that Protransf-CoQ10 could transform into transfersomal vesicles with particle sizes of approximately 201.5 ± 6.1 nm and a zeta potential of − 11.26 ± 5.14 mV. The dispersion of Protransf-CoQ10 into emulgel base resulted in stable Protransf-CoQ10 Emulgel during 28 days of observation at low temperatures. Moreover, the in vivo study revealed that Protransf-CoQ10 Emulgel successfully increases the collagen density and number of fibroblast cells in UV radiation skin-aged induced-mice which reflects its potential for repairing the skin ageing process. In addition, the 24-h topical application of Protransf-CoQ10 Emulgel showed that no erythema or skin rash was observed during the study. In conclusion, loading CoQ10 into protransfersomal Emulgel successfully enhanced the stability and anti-ageing efficacy enabling its potential use as anti-ageing cosmetics.
A retrospective study of sugammadex for reversal of neuromuscular blockade induced by rocuronium in critically ill patients in the ICU
Authors: Bologheanu Răzvan , Lichtenegger Paul , Maleczek Mathias , Laxar Daniel , Schaden Eva , Kimberger Oliver 
Published: January 2022

AbstractSugammadex has been approved for reversal of neuromuscular blockade by vecuronium and rocuronium in adults undergoing surgery. Although widely used in the operating room, sugammadex has not been investigated in the intensive care unit setting. This study aimed to evaluate the use of sugammadex in critically ill patients with a focus on known drug-related adverse reactions. In this single-center, retrospective, observational study, 91 critically ill patients who were administered sugammadex while in the ICU were evaluated. Electronic health records were reviewed, and baseline data, as well as indication and incidence of complications possibly related to sugammadex, were retrospectively collected. The most common procedures requiring neuromuscular blockade followed by reversal with sugammadex were bronchoscopy, percutaneous dilatative tracheostomy, and percutaneous endoscopic gastrostomy. Within 2 h following administration of sugammadex, skin rash and use of antihistamines were reported in 4 patients (4.4%) in total; bradycardia was observed in 9 patients (9.9%), and respiratory adverse events were described in 3 patients (3.3%). New-onset bleeding up to 24 h after sugammadex was reported in 7 patients (7.7%), 3of whom received transfusions of packed red blood cells. Sugammadex was well tolerated in critically ill patients and could be considered for reversal of neuromuscular blockade in this population. Larger prospective studies are required to determine the safety profile and evaluate the potential benefit and indications of sugammadex in the critical care setting.
A template-free, more environmentally friendly approach for glass micro-texturing
Authors: Jin Yuhui , Li Aize , Stewart Ross J. , Hancock Robert R. , Baker David E. , Yongsunthon Ruchirej , Hughes Kelleen K. , Weidman David L. 
Published: January 2022

AbstractMicron and nanometer size textured silicate glass surfaces are of interest in consumer electronics, photovoltaics, and biosensing applications. Typically, texturing glass surfaces requires applying a patterned mask or a pre-etching treatment (e.g. sandblasting) on the glass substrate, followed by a mask transferring or etching process using a fluoride-containing compound. The major challenges of such a process are the complexity and cost of masking, and the safety and environmental concerns around the usage and disposal of hydrofluoric acid. Here, we describe a template-free method to construct micron-sized and submicron-sized texture on isotropic glass surfaces in one step. The new texturing mechanisms are well supported by experimental data and peridynamic simulations. With this novel strategy, the etchant uses fluoride-free chemicals such as citric acid to texture silicate glass. Etchant concentration, etch temperature, time, and additives are the primary parameters that dictate the texturing process. Surface feature size and depth can be independently controlled by tuning the leaching and chemical polishing process. We hope this study can trigger more research on novel and more environmentally friendly texturing of isotropic materials.
Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein
Authors: Becerra Arturo , Muñoz-Velasco Israel , Aguilar-Cámara Abelardo , Cottom-Salas Wolfgang , Cruz-González Adrián , Vázquez-Salazar Alberto , Hernández-Morales Ricardo , Jácome Rodrigo , Campillo-Balderas José Alberto , Lazcano Antonio 
Published: January 2022

AbstractLow complexity regions (LCRs) are protein sequences formed by a set of compositionally biased residues. LCRs are extremely abundant in cellular proteins and have also been reported in viruses, where they may partake in evasion of the host immune system. Analyses of 28,231 SARS-CoV-2 whole proteomes and of 261,051 spike protein sequences revealed the presence of four extremely conserved LCRs in the spike protein of several SARS-CoV-2 variants. With the exception of Iota, where it is absent, the Spike LCR-1 is present in the signal peptide of 80.57% of the Delta variant sequences, and in other variants of concern and interest. The Spike LCR-2 is highly prevalent (79.87%) in Iota. Two distinctive LCRs are present in the Delta spike protein. The Delta Spike LCR-3 is present in 99.19% of the analyzed sequences, and the Delta Spike LCR-4 in 98.3% of the same set of proteins. These two LCRs are located in the furin cleavage site and HR1 domain, respectively, and may be considered hallmark traits of the Delta variant. The presence of the medically-important point mutations P681R and D950N in these LCRs, combined with the ubiquity of these regions in the highly contagious Delta variant opens the possibility that they may play a role in its rapid spread.