bluuebunny/crossref_metadata_2025_split huggingface dataset:
CellDART: Cell type inference by domain adaptation of single-cell and spatial transcriptomic data
Authors: Bae Sungwoo , Na Kwon Joong , Koh Jaemoon , Lee Dong Soo , Choi Hongyoon , Kim Young Tae 
Published: April 2021

AbstractDeciphering the cellular composition in genome-wide spatially resolved transcriptomic data is a critical task to clarify the spatial context of cells in a tissue. In this study, we developed a method, CellDART, which estimates the spatial distribution of cells defined by single-cell level data using domain adaptation of neural networks and applied it to the spatial mapping of human lung tissue. The neural network that predicts the cell proportion in a pseudospot, a virtual mixture of cells from single-cell data, is translated to decompose the cell types in each spatial barcoded region. First, CellDART was applied to mouse brain and human dorsolateral prefrontal cortex tissue to identify cell types with a layer-specific spatial distribution. Overall, the suggested approach was competent to the other computational methods in predicting the spatial localization of excitatory neurons. Besides, CellDART was capable of decomposing cellular proportion in mouse hippocampus Slide-seq data. Furthermore, CellDART elucidated the cell type predominance defined by the human lung cell atlas across the lung tissue compartments and it corresponded to the known prevalent cell types. CellDART is expected to help to elucidate the spatial heterogeneity of cells and their close interactions in various tissues.
The RNA m6A reader YTHDF2 controls NK cell anti-tumor and anti-viral immunity
Authors: Ma Shoubao , Yan Jiazhuo , Barr Tasha , Zhang Jianying , Chen Zhenhua , Wang Li-Shu , Sun Joseph C. , Chen Jianjun , Caligiuri Michael A , Yu Jianhua 
Published: April 2021

AbstractN6-methyladenosine (m6A) is the most prevalent post-transcriptional modification on RNA. NK cells are the predominant innate lymphoid cells that mediate anti-viral and anti-tumor immunity. However, whether and how m6A modifications affect NK cell immunity remains unknown. Here, we discover that YTHDF2, a well-known m6A reader, is upregulated in NK cells upon activation by cytokines, tumors, and cytomegalovirus infection.Ythdf2deficiency in NK cells impairs NK cell anti-tumor and anti-viral activityin vivo. YTHDF2 maintains NK cell homeostasis and terminal maturation, correlating with modulating NK cell trafficking and regulating Eomes, respectively. YTHDF2 promotes NK cell effector function and is required for IL-15-mediated NK cell survival and proliferation by forming a STAT5-YTHDF2 positive feedback loop. Transcriptome-wide screening identifiesTardbpto be involved in cell proliferation or survival as a YTHDF2-binding target in NK cells. Collectively, we elucidate the biological roles of m6A modifications in NK cells and highlight a new direction to harness NK cell anti-tumor immunity.
An Ohio State Scenic River Shows Elevated Antibiotic Resistance Genes, IncludingAcinetobacterTetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent
Authors: Murphy April , Barich Daniel , Fennessy Siobhan , Slonczewski Joan L. 
Published: April 2021

ABSTRACTThe entry of antibiotic resistance genes (ARGs) into aquatic systems has been documented for large municipal wastewater treatment plants, but there is less study of the impact of smaller plants that are situated on small rural rivers. We sampled water metagenomes for ARG and taxa composition from the Kokosing River, a small rural river in Knox County, Ohio, which has been designated an Ohio State Scenic River for retention of natural character. Samples were obtained 1.0 km upstream, 120 m downstream, and 6.4 km downstream from the effluent release of the Mount Vernon wastewater treatment plant (WWTP). ARGS were identified in metagenomes using ShortBRED markers from the CARD database screened against UniPROT. Through all seasons, the metagenome just downstream of the WWTP effluent showed a substantial elevation of at least 15 different ARGs, including 6 ARGs commonly associated withAcinetobacter baumanniisuch asmsrE, mphE(macrolide resistance) andtet(39) (tetracycline resistance). The ARGs most prevalent near the effluent pipe persisted 6.4 km downriver. Using MetaPhlAn2 clade-specific marker genes, the taxa distribution near the effluent showed elevation of reads annotated asAcinetobacterspecies as well as gut-associated taxa, Bacteroides and Firmicutes. The ARG levels and taxa prevalence showed little dependence on seasonal chlorination of the effluent. Nitrogen and phosphorus were elevated near the effluent pipe but had no consistent correlation with ARG levels. We show that in a rural river microbiome, year-round wastewater effluent substantially elevates ARGs including those associated with multidrug-resistantA. baumanii.IMPORTANCEAntibiotic resistance is a growing problem worldwide, with frequent transmission between pathogens and environmental organisms. Rural rivers can support high levels of recreational use by people unaware of inputs from treated wastewater, while WWTPs can generate a small but significant portion of flow volume into a river surrounded by forest and agriculture. There is little information on the rural impacts of WWTP effluent on the delivery and transport of antibiotic resistance genes. In our study, the river water proximal to wastewater effluent shows evidence for the influx of multidrug-resistantAcinetobacter baumanii, an opportunistic pathogen of concern for hospitals but also widespread in natural environments. Our work highlights the importance of wastewater effluent in management of environmental antibiotic resistance, even in high quality, rural river systems.
Rapid and simultaneous identification of three mutations by the Novaplex™ SARS-CoV-2 Variants I Assay kit
Authors: Kami Wakaki , Kinjo Takeshi , Arakaki Wakako , Oki Hiroya , Motooka Daisuke , Nakamura Shota , Fujita Jiro 
Published: April 2021

AbstractBackgroundThe emergence of SARS-CoV-2 variants has caused an unexpected rebound globally. The World Health Organization has listed three variants (B.1.1.7, B.1.351, and P.1) as variants of concern. To understand the epidemiology and thereby plan appropriate safety measures, differential identification of the variants is indeed critical.ObjectivesAlthough whole-genome sequencing is the gold standard for variant identification, it is time-consuming and relatively expensive. Therefore, a rapid, easy, and cost-effective platform targeting multiple regions of the genome is required. Here, we assessed the usefulness of the Novaplex™ SARS-CoV-2 Variants I Assay kit in identifying mutations in the variants.Study designWe retrospectively examined 30 stored nasal swabs from COVID-19-positive patients tested between November 2020 and March 2021. RNA extracted from these swabs was subjected to the commercial kit and real-time reverse transcription-PCR was performed. To determine the genome sequences of SARS-CoV-2 in the collected samples and deduce the consensus sequences among the identified variants, genome sequencing libraries were prepared and mapped to the reference genome.ResultsFour of the tested samples were determined as variants. Of them, two harbored both H69/V70 deletion and N501Y substitution, whereas two harbored E484K substitution alone.ConclusionsThe variant with E484K substitution alone (“R.1”) has been now categorized as a variant of interest in Japan. Additionally, the kit-based assay was found to be feasible, convenient, and user-friendly in identifying the abovementioned mutations with a turnaround time of only 2 hours.
Optimism and pessimism in optimised replay
Authors: Antonov Georgy , Gagne Christopher , Eldar Eran , Dayan Peter 
Published: April 2021

ABSTRACTThe replay of task-relevant trajectories is known to contribute to memory consolidation and improved task performance. A wide variety of experimental data show that the content of replayed sequences is highly specific and can be modulated by reward as well as other prominent task variables. However, the rules governing the choice of sequences to be replayed still remain poorly understood. One recent theoretical suggestion is that the prioritization of replay experiences in decision-making problems is based on their effect on the choice of action. We show that this implies that subjects should replay sub-optimal actions that they dysfunctionally choose rather than optimal ones, when, by being forgetful, they experience large amounts of uncertainty in their internal models of the world. We use this to account for recent experimental data demonstrating exactly pessimal replay, fitting model parameters to the individual subjects’ choices.
Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs
Authors: Schilling Johannes , Jost Christian , Ilie Ioana Mariuca , Schnabl Joachim , Buechi Oralea , Eapen Rohan S. , Truffer Rafaela , Caflisch Amedeo , Forrer Patrik 
Published: April 2021

AbstractDesigned Ankyrin Repeat Proteins (DARPins) are a class of antibody mimetics with a high and mostly unexplored potential in drug development. They are clinically validated and thus represent a true alternative to classical immunoglobulin formats. In contrast to immunoglobulins, they are built from solenoid protein domains comprising an N-terminal capping repeat, one or more internal repeats and a C-terminal capping repeat. By usingin silicoanalysis and a rationally guided Ala-Scan, we identified position 17 of the N-terminal capping repeat to play a key role for the overall protein thermostability. The melting temperature of a DARPin domain with a single full-consensus internal repeat was increased by about 8°C to 10°C when the original Asp17 was replaced by Leu, Val, Ile, Met, Ala or Thr, as shown by high-temperature unfolding experiments at equilibrium. We then transferred the Asp17Leu mutation to various backgrounds, including different N- and C-terminal capping repeats and clinically validated DARPin domains, such as the VEGF-binding ankyrin repeat domain of abicipar pegol. In all cases, the proteins remained monomeric and showed improvements in the thermostability of about 8°C to 16°C. Thus, the replacement of Asp17 seems to be generically applicable to this drug class. Molecular dynamics simulations show that the Asp17Leu mutation reduces electrostatic repulsion and improves van-der-Waals packing, rendering the DARPin domain less flexible and more stable. Interestingly, such a beneficial Asp17Leu mutation is present in the N-terminal caps of three of the five DARPin domains of ensovibep, a SARS-CoV-2 entry inhibitor currently in clinical development. This mutation is likely responsible, at least in part, for the very high melting temperature (>90°C) of this promising anti-Covid-19 drug. Overall, such N-terminal capping repeats with increased thermostability seem to be beneficial for the development of innovative drugs based on DARPins.
Activation of ACC synthase 2/6 increases stomatal density and cluster on theArabidopsisleaf epidermis during drought
Authors: Jia Ming-zhu , Liu Ling-yun , Geng Chen , Song Chun-peng , Jiang Jing 
Published: April 2021

AbstractIt is known that the transcription factor SPEECHLESS (SPCH) drives entry of epidermal cells into stomatal lineage, and that the activation of subtilisin-like protease SDD1 reduces stomatal density and cluster on the epidermis. However, there is still a big gap in our understanding of the relationship between stomatal development and the establishment of stomatal density and pattern, especially during drought. Interestingly, 1-aminocyclopropane-1-carboxylic acid (ACC) not only promotes stomatal development, but also is involved in the establishment of stomatal density and pattern. ACC generation comes from the activity of ACC synthase (ACS), while ACS activity could be mediated by drought. This work showed that the Arabidopsis SPCH activatedACS2/6expression and ACC-dependent stomatal generation with an increase of stomatal density and cluster under drought conditions; and the possible mechanisms were that ACC-induced Ca2+shortage in stomatal lineage reduced the inhibition of the transcription factor GT-2 Like 1 (GTL1) onSDD1expression. These suggest that ACS2/6-dependent ACC accumulation integrated stomatal development with the establishment of stomatal density and pattern by mediating Ca2+levels in stomatal lineage cells on the leaf epidermis, and this integration is directly related to the growth or survival of plants under escalated drought stress.HighlightACC synthase ACS2/6 activation integrated stomatal individual development with space setting between stomata by mediating Ca2+levels in stomatal lineage on the leaf epidermis in response to drought.
Long- and short-range bimodal signals mediate mate location and recognition in yellow fever mosquitoes
Authors: Ko Elton , Blake Adam J. , Lier Chiara , Takács Stephen , Gries Gerhard 
Published: April 2021

SummaryMate location and mate selection behavior in diurnally-active yellow fever mosquitoes,Aedes aegypti, take place in mating swarms but the mechanisms underlying swarm formation and long-range detection of females by males remain largely unexplored. In high-speed video recordings we show that incident light reflects off the wings of swarming males, and in behavioral experiments we demonstrate that swarm formation and mate recognition are mediated, in part, by these wingbeat light flashes and by wingbeat sound signals that operate at long and short range, respectively. To test for range-dependent effects of these signals, we presented ‘mating swarms’ in form of two paired 8-LED assemblies that were fitted with micro-speakers and placed either well separated in a large space or side-by-side in a small space. In the large but not the small space, the LED assembly flashing light at the wingbeat frequency of females (665 Hz), and emitting their wingbeat sound (665 Hz), attracted and prompted 5.8-times more alightings by males than the LED assembly emitting constant light and wingbeat sound. In the small space, the LED assembly flashing light and emitting wingbeat sound induced 5.0-times more alightings by males than the LED assembly flashing light without wingbeat sound. The attractiveness of light flash signals to males increased with increasing numbers of signals but did not vary according to their wavelengths (UV or blue). Females responded to light flash signals of males. As predicted by the sensory drive theory, light flashes had no signal function for crepuscular house mosquitoes,Culex pipiens.
Visualizing transcription sites in living cells using a genetically encoded probe specific for the elongating form of RNA polymerase II
Authors: Uchino Satoshi , Ito Yuma , Sato Yuko , Handa Tetsuya , Ohkawa Yasuyuki , Tokunaga Makio , Kimura Hiroshi 
Published: April 2021

AbstractIn eukaryotic nuclei, most genes are transcribed by RNA polymerase II (RNAP2). How RNAP2 transcription is regulated in the nucleus is a key to understanding the genome and cell function. The largest subunit of RNAP2 has a long heptapeptide repeat (Tyr1-Ser2-Pro3-Thr4-Ser5- Pro6-Ser7) at the C-terminal domain and Ser2 is phosphorylated on an elongation form of RNAP2. To detect RNAP2 Ser2 phosphorylation (RNAP2 Ser2ph) in living cells, we developed a genetically encoded modification-specific intracellular antibody (mintbody) probe. The RNAP2 Ser2ph-mintbody probe exhibited numerous foci, possibly representing transcription “factories” in living HeLa cells, and foci were diminished when cells were treated with triptolide to induce RNAP2 degradation and with flavopiridol to inhibit Ser2ph. An in vitro binding assay using phospho-peptides confirmed the Ser2ph-specific binding of the mintbody. These results support the view that mintbody localization represents the sites of RNAP2 Ser2ph in living cells. RNAP2 Ser2ph-mintbody foci were colocalized with proteins associated with elongating RNAP2, such as the CDK12 and Paf1 complex component, compared to factors involved in transcription activation around the transcription start sites, such as CDK9 and BRD4. Tracking analysis revealed that RNAP2 Ser2ph-mintbody foci showed constrained diffusional motion like chromatin, but was more mobile compared to euchromatin domains, suggesting that the elongating RNAP2 complexes are separated from the more confined initiating clusters.SummaryThe authors developed a genetically encoded probe to specifically detect the Ser2- phosphorylated, elongating form of RNA Polymerase II in living cells. The motion of Ser2- phosphorylated polymerase foci was more dynamic than chromatin domains, suggesting that the elongating complexes are separated from the more confined initiating clusters.
SMURF2 phosphorylation at Thr249 modifies the stemness and tumorigenicity of glioma stem cells by regulating TGF-β receptor stability
Authors: Hiraiwa Manami , Fukasawa Kazuya , Iezaki Takashi , Sabit Hemragul , Horie Tetsuhiro , Tokumura Kazuya , Iwahashi Sayuki , Murata Misato , Kobayashi Masaki , Park Gyujin , Kaneda Katsuyuki , Todo Tomoki , Hirao Atsushi , Nakada Mitsutoshi , Hinoi Eiichi 
Published: April 2021

AbstractGlioma stem cells (GSCs) contribute to the pathogenesis of glioblastoma, the most malignant form of glioma. The implication and underlying mechanisms of SMAD specific E3 ubiquitin protein ligase 2 (SMURF2) on the GSC phenotypes remain unknown. We previously demonstrated that SMURF2 phosphorylation at Thr249(SMURF2Thr249) activates its E3 ubiquitin ligase activity. Here, we demonstrate that SMURF2Thr249phosphorylation plays an essential role in maintaining GSC stemness and tumorigenicity.SMURF2silencing augmented the self-renewal potential and tumorgenicity of patient-derived GSCs. The SMURF2Thr249phosphorylation level was low in human glioblastoma pathology specimens. Introduction of theSMURF2T249Amutant resulted in increased stemness and tumorgenicity of GSCs, recapitulating theSMURF2silencing. Moreover, the inactivation of SMURF2Thr249phosphorylation increases TGF-β receptor (TGFBR) protein stability. Indeed,TGFBR1knockdown markedly counteracted the GSC phenotypes bySMURF2T249Amutant. These findings highlight the importance of SMURF2Thr249phosphorylation in maintaining GSC phenotypes, thereby demonstrating a potential target for GSC-directed therapy.
The metabolic cost of overcoming air resistive forces in distance running
Authors: da Silva Edson Soares , Kram Rodger , Hoogkamer Wouter 
Published: April 2021

AbstractWe lack a mechanistic understanding of the relationship between aerodynamic drag forces and metabolic power during running. Further, the energetic and time savings possible from reducing aerodynamic drag (drafting) are still unclear due to the different methods previously assumed for converting from force reductions to metabolic power savings. Here, we quantified how small horizontal impeding forces (equivalent to aerodynamic forces) affect metabolic power and ground reaction forces over a range of velocities in competitive runners. In three sessions, 12 runners completed six 5-minute trials with 5 minutes of recovery in-between. We tested one velocity per session (12, 14 and 16 km/h), at three horizontal impeding force conditions (0, 4 and 8 N). On average, metabolic power increased by 6.13% per 1% body weight of horizontal impeding force but varied considerably between individuals. With greater horizontal impeding force, braking impulses decreased while propulsive impulses increased (p < 0.001). Across running velocities, the changes in braking and propulsive impulses with greater impeding force were correlated (r = -0.97; p < 0.001), but were not related to individual changes in metabolic power. We estimate that at ∼2-hour marathon pace, overcoming air resistive force comprises 8.52% of the gross metabolic power on average.
Modulations in motor unit discharge are related to changes in fascicle length during isometric contractions
Authors: Martinez-Valdes Eduardo , Negro Francesco , Botter Alberto , Pincheira Patricio A , Cerone Giacinto Luigi , Falla Deborah , Lichtwark Glen A , Cresswell Andrew G 
Published: April 2021

ABSTRACTThe integration of electromyography (EMG) and ultrasound imaging has provided important information about the mechanisms of muscle activation and contraction. Unfortunately, EMG does not allow an accurate assessment of the interplay between the neural drive received by muscles, changes in fascicle length (FL) and the force/torque produced. We aimed to assess the relationship between modulations in tibialis anterior (TA) motor unit (MU) firing rate, FL and dorsiflexion torque (DT) using ultrasound-transparent high-density EMG electrodes. EMG and ultrasound images were recorded simultaneously from TA, using a 32-electrode silicon matrix, while performing isometric dorsiflexion, at diverse ankle joint positions (0° and 30° plantar flexion) and torques (20% and 40% of maximum). EMG signals were decomposed into individual MUs and changes in FL were assessed with a fascicle-tracking algorithm. MU firings were converted into a cumulative spike train (CST) that was cross-correlated with DT (CST-DT) and FL (CST-FL). High cross-correlations were found for CST-FL, 0.60 (range: 0.31-0.85) and CST-DT 0.71 (range: 0.31-0.88). Cross-correlation lags revealed that the delay between CST-FL (~75ms) was significantly smaller than CST-DT (~150ms, p<0.001). These delays affected the interpretation of MU recruitment/de-recruitment thresholds, with FL showing similar lengths for both recruitment and de-recruitment. This study is the first to demonstrate that changes in TA FL are closely related to both modulations in MU firing frequency and DT. These relationships allow assessment of the interplay between neural drive, muscle contraction and resultant torque, thereby providing a better understanding of the mechanisms responsible for the generation of muscle force.NEW AND NOTEWORTHYBy employing ultrasound-transparent high-density surface EMG electrodes, we show that modulations in tibialis anterior motor unit discharge rate were closely related to both changes in its fascicle length and resultant torque. These relationships allowed quantifying delays between neural drive and muscle shortening as well as muscle shortening and torque during submaximal isometric contractions, providing an accurate estimation of the time required to generate muscle force and subsequent production of torque via the tendon.