bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multivalency transforms SARS-CoV-2 antibodies into ultrapotent neutralizers
Authors: Rujas Edurne , Kucharska Iga , Tan Yong Zi , Benlekbir Samir , Cui Hong , Zhao Tiantian , Wasney Gregory A. , Budylowski Patrick , Guvenc Furkan , Newton Jocelyn C. , Sicard Taylor , Semesi Anthony , Muthuraman Krithika , Nouanesengsy Amy , Aschner Clare Burn , Prieto Katherine , Bueler Stephanie A. , Youssef Sawsan , Liao-Chan Sindy , Glanville Jacob , Christie-Holmes Natasha , Mubareka Samira , Gray-Owen Scott D. , Rubinstein John L. , Treanor Bebhinn , Julien Jean-Philippe 
Published: June 2021

AbstractSARS-CoV-2, the virus responsible for COVID-19, has caused a global pandemic. Antibodies can be powerful biotherapeutics to fight viral infections. Here, we use the human apoferritin protomer as a modular subunit to drive oligomerization of antibody fragments and transform antibodies targeting SARS-CoV-2 into exceptionally potent neutralizers. Using this platform, half-maximal inhibitory concentration (IC50) values as low as 9 × 10−14 M are achieved as a result of up to 10,000-fold potency enhancements compared to corresponding IgGs. Combination of three different antibody specificities and the fragment crystallizable (Fc) domain on a single multivalent molecule conferred the ability to overcome viral sequence variability together with outstanding potency and IgG-like bioavailability. The MULTi-specific, multi-Affinity antiBODY (Multabody or MB) platform thus uniquely leverages binding avidity together with multi-specificity to deliver ultrapotent and broad neutralizers against SARS-CoV-2. The modularity of the platform also makes it relevant for rapid evaluation against other infectious diseases of global health importance. Neutralizing antibodies are a promising therapeutic for SARS-CoV-2.
Radioisotope constraints of Arctic deep water export to the North Atlantic
Authors: Kipp Lauren E. , McManus Jerry F. , Kienast Markus 
Published: June 2021

AbstractThe export of deep water from the Arctic to the Atlantic contributes to the formation of North Atlantic Deep Water, a crucial component of global ocean circulation. Records of protactinium-231 (231Pa) and thorium-230 (230Th) in Arctic sediments can provide a measure of this export, but well-constrained sedimentary budgets of these isotopes have been difficult to achieve in the Arctic Ocean. Previous studies revealed a deficit of 231Pa in central Arctic sediments, implying that some 231Pa is either transported to the margins, where it may be removed in areas of higher particle flux, or exported from the Arctic via deep water advection. Here we investigate this “missing sink” of Arctic 231Pa and find moderately increased 231Pa deposition along Arctic margins. Nonetheless, we determine that most 231Pa missing from the central basin must be lost via advection into the Nordic Seas, requiring deep water advection of 1.1 – 6.4 Sv through Fram Strait.
The long lives of primates and the ‘invariant rate of ageing’ hypothesis
Authors: Colchero Fernando , Aburto José Manuel , Archie Elizabeth A. , Boesch Christophe , Breuer Thomas , Campos Fernando A. , Collins Anthony , Conde Dalia A. , Cords Marina , Crockford Catherine , Thompson Melissa Emery , Fedigan Linda M. , Fichtel Claudia , Groenenberg Milou , Hobaiter Catherine , Kappeler Peter M. , Lawler Richard R. , Lewis Rebecca J. , Machanda Zarin P. , Manguette Marie L. , Muller Martin N. , Packer Craig , Parnell Richard J. , Perry Susan , Pusey Anne E. , Robbins Martha M. , Seyfarth Robert M. , Silk Joan B. , Staerk Johanna , Stoinski Tara S. , Stokes Emma J. , Strier Karen B. , Strum Shirley C. , Tung Jenny , Villavicencio Francisco , Wittig Roman M. , Wrangham Richard W. , Zuberbühler Klaus , Vaupel James W. , Alberts Susan C. 
Published: June 2021

AbstractIs it possible to slow the rate of ageing, or do biological constraints limit its plasticity? We test the ‘invariant rate of ageing’ hypothesis, which posits that the rate of ageing is relatively fixed within species, with a collection of 39 human and nonhuman primate datasets across seven genera. We first recapitulate, in nonhuman primates, the highly regular relationship between life expectancy and lifespan equality seen in humans. We next demonstrate that variation in the rate of ageing within genera is orders of magnitude smaller than variation in pre-adult and age-independent mortality. Finally, we demonstrate that changes in the rate of ageing, but not other mortality parameters, produce striking, species-atypical changes in mortality patterns. Our results support the invariant rate of ageing hypothesis, implying biological constraints on how much the human rate of ageing can be slowed.
Supramolecular engineering of charge transfer in wide bandgap organic semiconductors with enhanced visible-to-NIR photoresponse
Authors: Yao Yifan , Ou Qi , Wang Kuidong , Peng Haijun , Fang Feier , Shi Yumeng , Wang Ye , Asperilla Daniel Iglesias , Shuai Zhigang , Samorì Paolo 
Published: June 2021

AbstractOrganic photodetectors displaying efficient photoelectric response in the near-infrared are typically based on narrow bandgap active materials. Unfortunately, the latter require complex molecular design to ensure sufficient light absorption in the near-infrared region. Here, we show a method combining an unconventional device architecture and ad-hoc supramolecular self-assembly to trigger the emergence of opto-electronic properties yielding to remarkably high near-infrared response using a wide bandgap material as active component. Our optimized vertical phototransistors comprising a network of supramolecular nanowires of N,N′-dioctyl-3,4,9,10-perylenedicarboximide sandwiched between a monolayer graphene bottom-contact and Au nanomesh scaffold top-electrode exhibit ultrasensitive light response to monochromatic light from visible to near-infrared range, with photoresponsivity of 2 × 105 A/W and 1 × 102 A/W, at 570 nm and 940 nm, respectively, hence outperforming devices based on narrow bandgap materials. Moreover, these devices also operate as highly sensitive photoplethysmography tool for health monitoring.
Controlling the pandemic during the SARS-CoV-2 vaccination rollout
Authors: Viana João , van Dorp Christiaan H. , Nunes Ana , Gomes Manuel C. , van Boven Michiel , Kretzschmar Mirjam E. , Veldhoen Marc , Rozhnova Ganna 
Published: June 2021

AbstractThere is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.
Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering
Authors: Lee Yunbeom , Kim Jong Goo , Lee Sang Jin , Muniyappan Srinivasan , Kim Tae Wu , Ki Hosung , Kim Hanui , Jo Junbeom , Yun So Ri , Lee Hyosub , Lee Kyung Won , Kim Seong Ok , Cammarata Marco , Ihee Hyotcherl 
Published: June 2021

AbstractUltrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.
Evidence for the Fulde–Ferrell–Larkin–Ovchinnikov state in bulk NbS2
Authors: Cho Chang-woo , Lyu Jian , Ng Cheuk Yin , He James Jun , Lo Kwan To , Chareev Dmitriy , Abdel-Baset Tarob A. , Abdel-Hafiez Mahmoud , Lortz Rolf 
Published: June 2021

AbstractWe present measurements of the magnetic torque, specific heat and thermal expansion of the bulk transition metal dichalcogenide (TMD) superconductor NbS2 in high magnetic fields, with its layer structure aligned strictly parallel to the field using a piezo rotary positioner. The upper critical field of superconducting TMDs in the 2D form is known to be dramatically enhanced by a special form of Ising spin orbit coupling. This Ising superconductivity is very robust to the Pauli paramagnetic effect and can therefore exist beyond the Pauli limit for superconductivity. We find that superconductivity beyond the Pauli limit still exists in bulk single crystals of NbS2 for a precisely parallel field alignment. However, the comparison of our upper critical field transition line with numerical simulations rather points to the development of a Fulde-Ferrell-Larkin-Ovchinnikov state above the Pauli limit as a cause. This is also consistent with the observation of a magnetic field driven phase transition in the thermodynamic quantities within the superconducting state near the Pauli limit.
Remote whispering metamaterial for non-radiative transceiving of ultra-weak sound
Authors: Zhang Jin , Rui Wei , Ma Chengrong , Cheng Ying , Liu Xiaojun , Christensen Johan 
Published: June 2021

AbstractTransceiving ultra-weak sound typically relies on signal pre-amplification at the transmitting end via active electro-acoustic devices, which inherently perturbs the environment in the form of noise that inevitably leads to information leakage. Here we demonstrate a passive remote-whispering metamaterial (RWM) enabling weak airborne sound at audible frequencies to reach unprecedented signal enhancement without altering the detected ambient soundscape, which is based on the extraordinary scattering properties of a metamaterial formed by a pair of self-resonating subwavelength Mie meta-cavities, constituting the acoustic analogy of Förster resonance energy transfer. We demonstrate efficient non-radiative sound transfer over distances hundreds times longer than the radius of the meta-cavities, which enables the RWM to recover weak sound signals completely overwhelmed by strong noise with enhanced signal-to-noise ratio from −3 dB below the detection limit of 0 dB in free space to 17.7 dB.
Proteomic analysis of chicken bone marrow-derived dendritic cells in response to an inactivated IBV + NDV poultry vaccine
Authors: van den Biggelaar Robin H. G. A. , van der Maas Larissa , Meiring Hugo D. , Pennings Jeroen L. A. , van Eden Willem , Rutten Victor P. M. G. , Jansen Christine A. 
Published: June 2021

AbstractInactivated poultry vaccines are subject to routine potency testing for batch release, requiring large numbers of animals. The replacement of in vivo tests for cell-based alternatives can be facilitated by the identification of biomarkers for vaccine-induced immune responses. In this study, chicken bone marrow-derived dendritic cells were stimulated with an inactivated vaccine for infectious bronchitis virus and Newcastle disease virus, as well as inactivated infectious bronchitis virus only, and lipopolysaccharides as positive control, or left unstimulated for comparison with the stimulated samples. Next, the cells were lysed and subjected to proteomic analysis. Stimulation with the vaccine resulted in 66 differentially expressed proteins associated with mRNA translation, immune responses, lipid metabolism and the proteasome. For the eight most significantly upregulated proteins, mRNA expression levels were assessed. Markers that showed increased expression at both mRNA and protein levels included PLIN2 and PSMB1. Stimulation with infectious bronchitis virus only resulted in 25 differentially expressed proteins, which were mostly proteins containing Src homology 2 domains. Stimulation with lipopolysaccharides resulted in 118 differentially expressed proteins associated with dendritic cell maturation and antimicrobial activity. This study provides leads to a better understanding of the activation of dendritic cells by an inactivated poultry vaccine, and identified PLIN2 and PSMB1 as potential biomarkers for cell-based potency testing.
A distributed saccade-associated network encodes high velocity conjugate and monocular eye movements in the zebrafish hindbrain
Authors: Leyden Claire , Brysch Christian , Arrenberg Aristides B. 
Published: June 2021

AbstractSaccades are rapid eye movements that redirect gaze. Their magnitudes and directions are tightly controlled by the oculomotor system, which is capable of generating conjugate, monocular, convergent and divergent saccades. Recent studies suggest a mainly monocular control of saccades in mammals, although the development of binocular control and the interaction of different functional populations is less well understood. For zebrafish, a well-established model in sensorimotor research, the nature of binocular control in this key oculomotor behavior is unknown. Here, we use the optokinetic response and calcium imaging to characterize how the developing zebrafish oculomotor system encodes the diverse repertoire of saccades. We find that neurons with phasic saccade-associated activity (putative burst neurons) are most frequent in dorsal regions of the hindbrain and show elements of both monocular and binocular encoding, revealing a mix of the response types originally hypothesized by Helmholtz and Hering. Additionally, we observed a certain degree of behavior-specific recruitment in individual neurons. Surprisingly, calcium activity is only weakly tuned to saccade size. Instead, saccade size is apparently controlled by a push–pull mechanism of opposing burst neuron populations. Our study reveals the basic layout of a developing vertebrate saccade system and provides a perspective into the evolution of the oculomotor system.
Surface mass balance analysis at Naradu Glacier, Western Himalaya, India
Authors: Kumar Rajesh , Singh Shruti , Singh Atar , Kumar Ramesh , Singh Shaktiman , Randhawa Surjeet Singh 
Published: June 2021

AbstractIn the present study, we analyze a field-based seven-year data series of surface mass-balance measurements collected during 2011/12 to 2017/18 on Naradu Glacier, western Himalaya, India. The average annual specific mass balance for the said period is  − 0.85 m w.e. with the maximum ablation of  − 1.15 m w.e. The analysis shows that the topographic features, south and southeast aspects and slopes between 7 to 24 degrees are the reasons behind the maximum ablation from a particular zone. The causes of surface mass balance variability have been analyzed through multiple linear regression analyses (MLRA) by taking temperature and precipitation as predictors. The MLRA demonstrates that 71% of the observed surface mass balance variance can be explained by temperature and precipitation. It clearly illustrates the importance of summer temperature, which alone explains 64% variance of surface mass balance. The seasonal analysis shows that most of the surface mass balance variability is described by summer temperature and winter precipitation as two predictor variables. Among monthly combinations, surface mass balance variance is best characterized by June temperature and September precipitation.
A reporter system for enriching CRISPR/Cas9 knockout cells in technically challenging settings like patient models
Authors: Liu Wen-Hsin , Völse Kerstin , Senft Daniela , Jeremias Irmela 
Published: June 2021

AbstractCRISPR/Cas9 represents a valuable tool to determine protein function, but technical hurdles limit its use in challenging settings such as cells unable to grow in vitro like primary leukemia cells and xenografts derived thereof (PDX). To enrich CRISPR/Cas9-edited cells, we improved a dual-reporter system and cloned the genomic target sequences of the gene of interest (GOI) upstream of an out-of-frame fluorochrome which was expressed only upon successful gene editing. To reduce rounds of in vivo passaging required for PDX leukemia growth, targets of 17 GOI were cloned in a row, flanked by an improved linker, and PDX cells were lentivirally transduced for stable expression. The reporter enriched scarce, successfully gene-edited PDX cells as high as 80%. Using the reporter, we show that KO of the SRC-family kinase LYN increased the response of PDX cells of B precursor cell ALL towards Vincristine, even upon heterozygous KO, indicating haploinsufficiency. In summary, our reporter system enables enriching KO cells in technically challenging settings and extends the use of gene editing to highly patient-related model systems.
Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing
Authors: Smith Aaron D. , Kamiński Marcin J. , Kanda Kojun , Sweet Andrew D. , Betancourt Julio L. , Holmgren Camille A. , Hempel Elisabeth , Alberti Federica , Hofreiter Michael 
Published: June 2021

AbstractThe study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.
A systematic review and meta-analysis of surgical morbidity of primary versus patch repaired congenital diaphragmatic hernia patients
Authors: Heiwegen Kim , de Blaauw Ivo , Botden Sanne M. B. I. 
Published: June 2021

AbstractLarge studies comparing the surgical outcome of primary versus patch repair in congenital diaphragmatic hernia (CDH) patients are rare. This study aims to evaluate the incidence of surgical complications in both types of CDH repair. PubMed, EMBASE, Cochrane and Web of Science were searched for peer-reviewed articles. Studies on CDH between 1991 and August 2020 were systematically screened and meta-analyses were performed. Primary outcomes of this review were: haemorrhage, chylothorax, recurrences and small bowel obstruction (SBO). A total of 6436 abstracts were screened, after which 25 publications were included (2910 patients). Patch repaired patients have a 2.8 times higher risk on developing a recurrence (20 studies) and a 2.5 times higher risk on developing a chylothorax (five studies). Moreover, they have a two times higher risk on developing a SBO. No studies could be included that evaluated the incidence of surgical haemorrhage between these patients. Although the quality of the studies was relatively low, patch repaired patients have a higher risk on developing a recurrence, chylothorax and small bowel obstruction. Large prospective studies are required to adjust for severity of disease, to reveal the true causative factors in order to minimize the risk on these surgical complications in both types of patients.
Mutant p53s and chromosome 19 microRNA cluster overexpression regulate cancer testis antigen expression and cellular transformation in hepatocellular carcinoma
Authors: Jinesh Goodwin G. , Napoli Marco , Smallin Marian T. , Davis Andrew , Ackerman Hayley D. , Raulji Payal , Montey Nicole , Flores Elsa R. , Brohl Andrew S. 
Published: June 2021

AbstractA subset of hepatocellular carcinoma (HCC) overexpresses the chromosome 19 miRNA cluster (C19MC) and is associated with an undifferentiated phenotype marked by overexpression of cancer testis antigens (CTAs) including anti-apoptotic melanoma-A antigens (MAGEAs). However, the regulation of C19MC miRNA and MAGEA expression in HCCs are not understood. Here we show that, C19MC overexpression is tightly linked to a sub-set of HCCs with transcription-incompetent p53. Using next-generation and Sanger sequencing we found that, p53 in Hep3B cells is impaired by TP53-FXR2 fusion, and that overexpression of the C19MC miRNA-520G in Hep3B cells promotes the expression of MAGEA-3, 6 and 12 mRNAs. Furthermore, overexpression of p53-R175H and p53-R273H mutants promote miR-520G and MAGEA RNA expression and cellular transformation. Moreover, IFN-γ co-operates with miR-520G to promote MAGEA expression. On the other hand, metals such as nickel and zinc promote miR-526B but not miR-520G, to result in the suppression of MAGEA mRNA expression, and evoke cell death through mitochondrial membrane depolarization. Therefore our study demonstrates that a MAGEA-promoting network involving miR-520G, p53-defects and IFN-γ that govern cellular transformation and cell survival pathways, but MAGEA expression and survival are counteracted by nickel and zinc combination.
2D weak anti-localization in thin films of the topological semimetal Pd$$_{3}$$Bi$$_{2}$$S$$_{2}$$
Authors: Shama  , Gopal R. K. , Sheet Goutam , Singh Yogesh 
Published: June 2021

AbstractPd$$_{3}$$

3

Bi$$_{2}$$

2

S$$_{2}$$

2

(PBS) is a recently proposed topological semimetal candidate. However, evidence for topological surface states have not yet been revealed in transport measurements due to the large mobility of bulk carriers. We report the growth and magneto-transport studies of PBS thin films where the mobility of the bulk carriers is reduced by two orders of magnitude, revealing for the first time, contributions from the 2-dimensional (2D) topological surface states in the observation of the 2D weak anti-localization (WAL) effect in magnetic field and angle dependent conductivity measurements. The magnetotransport data is analysed within the 2D Hikami-Larkin-Nagaoka (HLN) theory. The analysis suggests that multiple conduction channels contribute to the transport. It is also found that the temperature dependence of the dephasing length can’t be explained only by electron-electron scattering and that electron-phonon scattering also contributes to the phase relaxation mechanism in PBS films.