bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of phosphoenolpyruvate carboxykinase 1 as a potential therapeutic target for pancreatic cancer
Authors: Zhu Xiao-ren , Peng Shi-qing , Wang Le , Chen Xiao-yu , Feng Chun-xia , Liu Yuan-yuan , Chen Min-bin
Published: October 2021

Pancreatic cancer is the third leading cause of cancer-related mortalities and is characterized by rapid disease progression. Identification of novel therapeutic targets for this devastating disease is important. Phosphoenolpyruvate carboxykinase 1 (PCK1) is the rate-limiting enzyme of gluconeogenesis. The current study tested the expression and potential functions of PCK1 in pancreatic cancer. We show that PCK1 mRNA and protein levels are significantly elevated in human pancreatic cancer tissues and cells. In established and primary pancreatic cancer cells, PCK1 silencing (by shRNA) or CRISPR/Cas9-induced PCK1 knockout potently inhibited cell growth, proliferation, migration and invasion, and induced robust apoptosis activation. Conversely, ectopic overexpression of PCK1 in pancreatic cancer cells accelerated cell proliferation and migration. RNA-seq analyzing of differentially expressed genes (DEGs) in PCK1-silenced pancreatic cancer cells implied that DEGs were enriched in the PI3K-Akt-mTOR cascade. In pancreatic cancer cells, Akt-mTOR activation was largely inhibited by PCK1 shRNA, but was augmented after ectopic PCK1 overexpression. In vivo, the growth of PCK1 shRNA-bearing PANC-1 xenografts was largely inhibited in nude mice. Akt-mTOR activation was suppressed in PCK1 shRNA-expressing PANC-1 xenograft tissues. Collectively, PCK1 is a potential therapeutic target for pancreatic cancer.
SARS-CoV-2 binding and neutralizing antibody levels after Ad26.COV2.S vaccination predict durable protection in rhesus macaques
Authors: Roozendaal Ramon , Solforosi Laura , Stieh Daniel J. , Serroyen Jan , Straetemans Roel , Dari Anna , Boulton Muriel , Wegmann Frank , Rosendahl Huber Sietske K. , van der Lubbe Joan E. M. , Hendriks Jenny , Le Gars Mathieu , Dekking Liesbeth , Czapska-Casey Dominika N. , Guimera Nuria , Janssen Sarah , Tete Sarah , Chandrashekar Abishek , Mercado Noe B. , Yu Jingyou , Koudstaal Wouter , Perez-Ruixo Juan J. , Sadoff Jerry , Barouch Dan H. , Schuitemaker Hanneke , Zahn Roland
Published: October 2021

Several COVID-19 vaccines have recently gained authorization for emergency use. Limited knowledge on duration of immunity and efficacy of these vaccines is currently available. Data on other coronaviruses after natural infection suggest that immunity to SARS-CoV-2 might be short-lived, and preliminary evidence indicates waning antibody titers following SARS-CoV-2 infection. In this work, we model the relationship between immunogenicity and protective efficacy of a series of Ad26 vectors encoding stabilized variants of the SARS-CoV-2 Spike protein in rhesus macaques and validate the analyses by challenging macaques 6 months after immunization with the Ad26.COV2.S vaccine candidate that has been selected for clinical development. We show that Ad26.COV2.S confers durable protection against replication of SARS-CoV-2 in the lungs that is predicted by the levels of Spike-binding and neutralizing antibodies, indicating that Ad26.COV2.S could confer durable protection in humans and immunological correlates of protection may enable the prediction of durability of protection.
Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors
Authors: Gavin Amanda L. , Huang Deli , Blane Tanya R. , Thinnes Therese C. , Murakami Yusuke , Fukui Ryutaro , Miyake Kensuke , Nemazee David
Published: October 2021

Phospholipase D3 (PLD3) and PLD4 polymorphisms have been associated with several important inflammatory diseases. Here, we show that PLD3 and PLD4 digest ssRNA in addition to ssDNA as reported previously. Moreover,Pld3−/−Pld4−/−mice accumulate small ssRNAs and develop spontaneous fatal hemophagocytic lymphohistiocytosis (HLH) characterized by inflammatory liver damage and overproduction of Interferon (IFN)-γ. Pathology is rescued inUnc93b13d/3dPld3−/−Pld4−/−mice, which lack all endosomal TLR signaling; genetic codeficiency or antibody blockade of TLR9 or TLR7 ameliorates disease less effectively, suggesting that both RNA and DNA sensing by TLRs contributes to inflammation. IFN-γ made a minor contribution to pathology. Elevated type I IFN and some other remaining perturbations inUnc93b13d/3dPld3−/−Pld4−/−mice requires STING (Tmem173). Our results show that PLD3 and PLD4 regulate both endosomal TLR and cytoplasmic/STING nucleic acid sensing pathways and have implications for the treatment of nucleic acid-driven inflammatory disease.
A standardized genome architecture for bacterial synthetic biology (SEGA)
Authors: Bayer Carolyn N. , Rennig Maja , Ehrmann Anja K. , Nørholm Morten H. H.
Published: October 2021

Chromosomal recombinant gene expression offers a number of advantages over plasmid-based synthetic biology. However, the methods applied for bacterial genome engineering are still challenging and far from being standardized. Here, in an attempt to realize the simplest recombinant genome technology imaginable and facilitate the transition from recombinant plasmids to genomes, we create a simplistic methodology and a comprehensive strain collection called the Standardized Genome Architecture (SEGA). In its simplest form, SEGA enables genome engineering by combining only two reagents: a DNA fragment that can be ordered from a commercial vendor and a stock solution of bacterial cells followed by incubation on agar plates. Recombinant genomes are identified by visual inspection using green-white colony screening akin to classical blue-white screening for recombinant plasmids. The modular nature of SEGA allows precise multi-level control of transcriptional, translational, and post-translational regulation. The SEGA architecture simultaneously supports increased standardization of genetic designs and a broad application range by utilizing well-characterized parts optimized for robust performance in the context of the bacterial genome. Ultimately, its adaption and expansion by the scientific community should improve predictability and comparability of experimental outcomes across different laboratories.
Theory and simulations of condensin mediated loop extrusion in DNA
Authors: Takaki Ryota , Dey Atreya , Shi Guang , Thirumalai D.
Published: October 2021

Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular biological phenomenon. This process is driven by the formation of chromosome loops. The ATP consuming motor, condensin, interacts with chromatin segments to actively extrude loops. Motivated by real-time imaging of loop extrusion (LE), we created an analytically solvable model, predicting the LE velocity and step size distribution as a function of external load. The theory fits the available experimental data quantitatively, and suggests that condensin must undergo a large conformational change, induced by ATP binding, bringing distant parts of the motor to proximity. Simulations using a simple model confirm that the motor transitions between an open and a closed state in order to extrude loops by a scrunching mechanism, similar to that proposed in DNA bubble formation during bacterial transcription. Changes in the orientation of the motor domains are transmitted over ~50 nm, connecting the motor head and the hinge, thus providing an allosteric basis for LE.
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth–gut axis
Authors: Prasoodanan P. K. Vishnu , Sharma Ashok K. , Mahajan Shruti , Dhakan Darshan B. , Maji Abhijit , Scaria Joy , Sharma Vineet K.
Published: October 2021

The abundance and diversity of host-associated Prevotella species have a profound impact on human health. To investigate the composition, diversity, and functional roles of Prevotella in the human gut, a population-wide analysis was carried out on 586 healthy samples from western and non-western populations including the largest Indian cohort comprising of 200 samples, and 189 Inflammatory Bowel Disease samples from western populations. A higher abundance and diversity of Prevotella copri species enriched in complex plant polysaccharides metabolizing enzymes, particularly pullulanase containing polysaccharide-utilization-loci (PUL), were found in Indian and non-western populations. A higher diversity of oral inflammations-associated Prevotella species and an enrichment of virulence factors and antibiotic resistance genes in the gut microbiome of western populations speculates an existence of a mouth-gut axis. The study revealed the landscape of Prevotella composition in the human gut microbiome and its impact on health in western and non-western populations.
A novel random forest approach to revealing interactions and controls on chlorophyll concentration and bacterial communities during coastal phytoplankton blooms
Authors: Cheng Yiwei , Bhoot Ved N. , Kumbier Karl , Sison-Mangus Marilou P. , Brown James B. , Kudela Raphael , Newcomer Michelle E.
Published: October 2021

Increasing occurrence of harmful algal blooms across the land–water interface poses significant risks to coastal ecosystem structure and human health. Defining significant drivers and their interactive impacts on blooms allows for more effective analysis and identification of specific conditions supporting phytoplankton growth. A novel iterative Random Forests (iRF) machine-learning model was developed and applied to two example cases along the California coast to identify key stable interactions: (1) phytoplankton abundance in response to various drivers due to coastal conditions and land-sea nutrient fluxes, (2) microbial community structure during algal blooms. In Example 1, watershed derived nutrients were identified as the least significant interacting variable associated with Monterey Bay phytoplankton abundance. In Example 2, through iRF analysis of field-based 16S OTU bacterial community and algae datasets, we independently found stable interactions of prokaryote abundance patterns associated with phytoplankton abundance that have been previously identified in laboratory-based studies. Our study represents the first iRF application to marine algal blooms that helps to identify ocean, microbial, and terrestrial conditions that are considered dominant causal factors on bloom dynamics.
A weight regain of 1.5 kg or more and lack of exercise are associated with nonalcoholic fatty liver disease recurrence in men
Authors: Nakanishi Naoko , Hashimoto Yoshitaka , Okamura Takuro , Ohbora Akihiro , Kojima Takao , Hamaguchi Masahide , Fukui Michiaki
Published: October 2021

The importance of maintaining the remission of nonalcoholic fatty liver disease (NAFLD) has been overlooked. Here we aimed to clarify factors causing NAFLD recurrence. In this retrospective cohort study over 10.8 ± 5.4 years, we investigated 1260 male health check-up participants diagnosed with NAFLD who achieved remission. The data were compared between the maintained remission and recurrence group. Among all participants, 618 (49.0%) showed NAFLD recurrence at the last visit. Participants in the maintained remission group continued to lose weight (72.7 ± 9.1, 68.7 ± 8.5 and 68.2 ± 8.9 kg), whereas those in the recurrence group lost and regained weight (72.9 ± 9.9, 69.7 ± 9.3 and 73.0 ± 10.4 kg). Receiver operating characteristic curve analysis showed a weight regain of + 1.5 kg as the cutoff value for recurrence. The proportion of regular exercisers at the last visit was 34.6% in the maintained remission group and 24.5% in the recurrence group (p < 0.0001). Multivariable analysis revealed the amount of weight regain (in 1 kg increments; adjusted odds ratio, 1.29; 95% confidence interval, 1.24–1.34) and regular exercise at the last visit (adjusted odds ratio, 0.67; 95% confidence interval, 0.55–0.89) were independently associated with recurrence. These findings demonstrate a weight regain of 1.5 kg or more and lack of exercise were associated with NAFLD recurrence.
A smart mask for active defense against airborne pathogens
Authors: Kalavakonda Rohan Reddy , Masna Naren Vikram Raj , Mandal Soumyajit , Bhunia Swarup
Published: October 2021

Face masks are a primary preventive measure against airborne pathogens. Thus, they have become one of the keys to controlling the spread of the COVID-19 virus. Common examples, including N95 masks, surgical masks, and face coverings, are passive devices that minimize the spread of suspended pathogens by inserting an aerosol-filtering barrier between the user’s nasal and oral cavities and the environment. However, the filtering process does not adapt to changing pathogen levels or other environmental factors, which reduces its effectiveness in real-world scenarios. This paper addresses the limitations of passive masks by proposing ADAPT, a smart IoT-enabled “active mask”. This wearable device contains a real-time closed-loop control system that senses airborne particles of different sizes near the mask by using an on-board particulate matter (PM) sensor. It then intelligently mitigates the threat by using mist spray, generated by a piezoelectric actuator, to load nearby aerosol particles such that they rapidly fall to the ground. The system is controlled by an on-board micro-controller unit that collects sensor data, analyzes it, and activates the mist generator as necessary. A custom smartphone application enables the user to remotely control the device and also receive real-time alerts related to recharging, refilling, and/or decontamination of the mask before reuse. Experimental results on a working prototype confirm that aerosol clouds rapidly fall to the ground when the mask is activated, thus significantly reducing PM counts near the user. Also, usage of the mask significantly increases local relative humidity levels.
Probing the distinct chemosensitivity of Plasmodium vivax liver stage parasites and demonstration of 8-aminoquinoline radical cure activity in vitro
Authors: Maher Steven P. , Vantaux Amélie , Chaumeau Victor , Chua Adeline C. Y. , Cooper Caitlin A. , Andolina Chiara , Péneau Julie , Rouillier Mélanie , Rizopoulos Zaira , Phal Sivchheng , Piv Eakpor , Vong Chantrea , Phen Sreyvouch , Chhin Chansophea , Tat Baura , Ouk Sivkeng , Doeurk Bros , Kim Saorin , Suriyakan Sangrawee , Kittiphanakun Praphan , Awuku Nana Akua , Conway Amy J. , Jiang Rays H. Y. , Russell Bruce , Bifani Pablo , Campo Brice , Nosten François , Witkowski Benoît , Kyle Dennis E.
Published: October 2021

Improved control of Plasmodium vivax malaria can be achieved with the discovery of new antimalarials with radical cure efficacy, including prevention of relapse caused by hypnozoites residing in the liver of patients. We screened several compound libraries against P. vivax liver stages, including 1565 compounds against mature hypnozoites, resulting in one drug-like and several probe-like hits useful for investigating hypnozoite biology. Primaquine and tafenoquine, administered in combination with chloroquine, are currently the only FDA-approved antimalarials for radical cure, yet their activity against mature P. vivax hypnozoites has not yet been demonstrated in vitro. By developing an extended assay, we show both drugs are individually hypnozonticidal and made more potent when partnered with chloroquine, similar to clinically relevant combinations. Post-hoc analyses of screening data revealed excellent performance of ionophore controls and the high quality of single point assays, demonstrating a platform able to support screening of greater compound numbers. A comparison of P. vivax liver stage activity data with that of the P. cynomolgi blood, P. falciparum blood, and P. berghei liver stages reveals overlap in schizonticidal but not hypnozonticidal activity, indicating that the delivery of new radical curative agents killing P. vivax hypnozoites requires an independent and focused drug development test cascade.
Effect of straw reinforcement on the shearing and creep behaviours of Quaternary loess
Authors: Xue Zhong-Fei , Cheng Wen-Chieh , Wang Lin
Published: October 2021

In addition to the shearing behavior of soil, the creep character is also considered crucial in determining the long-term shear strength. This especially holds true for the loess that possesses the metastable microstructure and is prone to landslide hazards. This study explored the potential application of straw reinforcement to enhance the shearing and creep properties of the Quaternary loess. The mechanism responsible for the straw reinforcement to elevate the peak shear strength was revealed. Furthermore, three creep characters, namely attenuating creep, non-attenuating creep, and viscous flow were identified in this study. The unreinforced and reinforced specimen behaved in a different manner under identical shear stress ratio condition. The reinforced specimen was superior in limiting the particle relative movement within the shear plane than the unreinforced specimen. The chain reaction of interparticle contact loss, accompanied with excessive viscous displacement, rapid weakening of creep resistance, and eventually accelerated creep displacement, provided an evidence for the formation mechanism of slow-moving landslide. The long-term shear strength using the isochronal stress–strain relationship may be used for optimising the design of high-fill embankment works.
Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents
Authors: Anders Jason L. , Moustafa Mohamed Abdallah Mohamed , Mohamed Wessam Mohamed Ahmed , Hayakawa Takashi , Nakao Ryo , Koizumi Itsuro
Published: October 2021

Host–microbe interactions within the gastrointestinal tract (GIT) play a pivotal role in shaping host physiology, ecology, and life history. However, these interactions vary across gut regions due to changes in the physical environment or host immune system activity, thereby altering the microbial community. Each animal species may harbor their own unique microbial community due to host species-specific ecological traits such as dietary habits, micro-habitat preferences, and mating behavior as well as physiological traits. While the gut microbiota in wild animals has received much attention over the last decade, most studies comparing closely related species only utilized fecal or colon samples. In this study, we first compared the gut microbial community from the small intestine, cecum, colon, and rectum within three sympatric species of wild rodents (i.e. Apodemus speciosus, A. argenteus, and Myodes rufocanus). We then compared each gut region among host species to determine the effect of both gut region and host species on the gut microbiota. We found that the small intestine harbored a unique microbiome as compared to the lower GIT in all three host species, with the genus Lactobacillus in particular having higher abundance in the small intestine of all three host species. There were clear interspecific differences in the microbiome within all gut regions, although some similarity in alpha diversity and community structure within the small intestine was found. Finally, fecal samples may be appropriate for studying the lower GIT in these species, but not the small intestine.
Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production
Authors: Ijoma Grace N. , Nkuna Rosina , Mutungwazi Asheal , Rashama Charles , Matambo Tonderayi S.
Published: October 2021

An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.
Analysis and design of diode physical limit bandwidth efficient rectification circuit for maximum flat efficiency, wide impedance, and efficiency bandwidths
Authors: Gyawali Babita , Thapa Samundra K. , Barakat Adel , Yoshitomi Kuniaki , Pokharel Ramesh K.
Published: October 2021

Generally, a conventional voltage doubler circuit possesses a large variation of its input impedance over the bandwidth, which results in limited bandwidth and low RF-dc conversion efficiency. A basic aspect for designing wideband voltage doubler rectifiers is the use of complex matching circuits to achieve decade and octave impedance and RF-dc conversion efficiency bandwidths. Still, the reported techniques till now have been accompanied by a large fluctuation of the RF-dc conversion efficiency over the operating bandwidth. In this paper, we propose a novel rectification circuit with minimal inter-stage matching that consists of a single short-circuit stub and a virtual battery, which contributes negligible losses and overcomes these existing problems. Consequently, the proposed rectifier circuit achieves a diode physical-limit-bandwidth efficient rectification. In other words, the rectification bandwidth, as well as the peak efficiency, are controlled by the length of the stub and the physical limitation of the diodes.
NL-VTON: a non-local virtual try-on network with feature preserving of body and clothes
Authors: Tan Ze Lin , Bai Jing , Zhang Shao Min , Qin Fei Wei
Published: October 2021

In an image based virtual try-on network, both features of the target clothes and the input human body should be preserved. However, current techniques failed to solve the problems of blurriness on complex clothes details and artifacts on human body occlusion regions at the same time. To tackle this issue, we propose a non-local virtual try-on network NL-VTON. Considering that convolution is a local operation and limited by its convolution kernel size and rectangular receptive field, which is unsuitable for large size non-rigid transformations of persons and clothes in virtual try-on, we introduce a non-local feature attention module and a grid regularization loss so as to capture detailed features of complex clothes, and design a human body segmentation prediction network to further alleviate the artifacts on occlusion regions. The quantitative and qualitative experiments based on the Zalando dataset demonstrate that our proposed method significantly improves the ability to preserve features of bodies and clothes compared with the state-of-the-art methods.
Decrease in volume and density of foraminiferal shells with progressing ocean acidification
Authors: Kuroyanagi Azumi , Irie Takahiro , Kinoshita Shunichi , Kawahata Hodaka , Suzuki Atsushi , Nishi Hiroshi , Sasaki Osamu , Takashima Reishi , Fujita Kazuhiko
Published: October 2021

Rapid increases in anthropogenic atmospheric CO2 partial pressure have led to a decrease in the pH of seawater. Calcifying organisms generally respond negatively to ocean acidification. Foraminifera are one of the major carbonate producers in the ocean; however, whether calcification reduction by ocean acidification affects either foraminiferal shell volume or density, or both, has yet to be investigated. In this study, we cultured asexually reproducing specimens of Amphisorus kudakajimensis, a dinoflagellate endosymbiont-bearing large benthic foraminifera (LBF), under different pH conditions (pH 7.7–8.3, NBS scale). The results suggest that changes in seawater pH would affect not only the quantity (i.e., shell volume) but also the quality (i.e., shell density) of foraminiferal calcification. We proposed that pH and temperature affect these growth parameters differently because (1) they have differences in the contribution to the calcification process (e.g., Ca2+-ATPase and Ω) and (2) pH mainly affects calcification and temperature mainly affects photosynthesis. Our findings also suggest that, under the IPCC RCP8.5 scenario, both ocean acidification and warming will have a significant impact on reef foraminiferal carbonate production by the end of this century, even in the tropics.
Feasibility study and direct extraction of endogenous free metallic cations combining hemodialysis and chelating polymer
Authors: Natuzzi Marco , Grange Coralie , Gréa Thomas , Brichart Thomas , Aigle Axel , Bechet Denise , Hautefeuille Benoit , Thomas Eloise , Ayoub Jean-Yves , Bonnet Jeanne-Marie , Louzier Vanessa , Allaouchiche Bernard , Couturier Aymeric , Montembault Alexandra , de Oliveira Paula Nunes , David Laurent , Lux François , Tillement Olivier
Published: October 2021

In this article, we report the conception and the use of dialysis-based medical device for the extraction of metals. The medical device is obtained by addition in the dialysate of a functionalized chitosan that can chelate endogenous metals like iron or copper. This water-soluble functionalized chitosan is obtained after controlled reacetylation and grafting of DOTAGA. Due to the high mass of chitosan, the polymer cannot cross through the membrane and the metals are trapped in the dialysate during hemodialysis. Copper extraction has been evaluated in vitro using an hemodialysis protocol. Feasibility study has been performed on healthy sheep showing no acute toxicity througout the entire dialysis procedure and first insights of metallic extraction even on healthy animals.
Deterring non-target birds from toxic bait sites for wild pigs
Authors: Snow Nathan P. , Halseth Joseph M. , Foster Justin A. , Lavelle Michael J. , Fischer Justin W. , Glow Michael P. , Messer Ingrid A. , Cook Seth M. , VerCauteren Kurt C.
Published: October 2021

Toxic baiting of wild pigs (Sus scrofa) is a potential new tool for population control and damage reduction in the US. Field trials testing a prototype toxic bait (HOGGONE 2 containing 5% sodium nitrite [SN]), though, revealed that wild pigs spilled small particles of toxic bait outside of bait stations which subsequently created hazards for non-target species that consumed those particles, primarily passerine birds. To deter non-target birds from consuming particles of spilled bait, we tested four deterrents at mock bait sites (i.e., baited with bird seed) in north-central Colorado, USA during April–May 2020. We found a programable, inflatable deterrent device (scare dancer) reduced bird visitation by an average of 96%. Then, we evaluated the deterrent devices at SN-toxic bait sites in north-central Texas, USA during July 2020, where the devices were activated the morning following deployment of SN-toxic bait. Overall, we found 139 dead wild pigs at 10 bait sites following one night of toxic baiting, which represented an average of 91% reduction in wild pigs visiting bait sites. We found that deterrent devices were 100% effective at deterring birds from toxic bait sites. We found two dead non-target mice at bait sites without deterrent devices. We noted that deploying toxic bait in mid-summer rather than late-winter/early-spring reduced hazards to migrating birds because they were not present in our study area during July. We recommend using deterrent devices (i.e., novel, programmable, battery operated, continuous and erratic movement, and snapping sounds) to reduce hazards to non-target birds at SN-toxic bait sites. We further recommend deploying SN-toxic bait during seasons when migrating birds are not as abundant until further research demonstrates minimal risks to migrating birds.
Biological data annotation via a human-augmenting AI-based labeling system
Authors: van der Wal Douwe , Jhun Iny , Laklouk Israa , Nirschl Jeff , Richer Lara , Rojansky Rebecca , Theparee Talent , Wheeler Joshua , Sander Jörg , Feng Felix , Mohamad Osama , Savarese Silvio , Socher Richard , Esteva Andre
Published: October 2021

Biology has become a prime area for the deployment of deep learning and artificial intelligence (AI), enabled largely by the massive data sets that the field can generate. Key to most AI tasks is the availability of a sufficiently large, labeled data set with which to train AI models. In the context of microscopy, it is easy to generate image data sets containing millions of cells and structures. However, it is challenging to obtain large-scale high-quality annotations for AI models. Here, we present HALS (Human-Augmenting Labeling System), a human-in-the-loop data labeling AI, which begins uninitialized and learns annotations from a human, in real-time. Using a multi-part AI composed of three deep learning models, HALS learns from just a few examples and immediately decreases the workload of the annotator, while increasing the quality of their annotations. Using a highly repetitive use-case—annotating cell types—and running experiments with seven pathologists—experts at the microscopic analysis of biological specimens—we demonstrate a manual work reduction of 90.60%, and an average data-quality boost of 4.34%, measured across four use-cases and two tissue stain types.
Monitoring of compound resting membrane potentials of cell cultures with ratiometric genetically encoded voltage indicators
Authors: Rühl Philipp , Langner Johanna M. , Reidel Jasmin , Schönherr Roland , Hoshi Toshinori , Heinemann Stefan H.
Published: October 2021

The cellular resting membrane potential (Vm) not only determines electrical responsiveness of excitable cells but also plays pivotal roles in non-excitable cells, mediating membrane transport, cell-cycle progression, and tumorigenesis. Studying these processes requires estimation of Vm, ideally over long periods of time. Here, we introduce two ratiometric genetically encoded Vm indicators, rArc and rASAP, and imaging and analysis procedures for measuring differences in average resting Vm between cell groups. We investigated the influence of ectopic expression of K+ channels and their disease-causing mutations involved in Andersen-Tawil (Kir2.1) and Temple-Baraitser (KV10.1) syndrome on median resting Vm of HEK293T cells. Real-time long-term monitoring of Vm changes allowed to estimate a 40–50 min latency from induction of transcription to functional Kir2.1 channels in HEK293T cells. The presented methodology is readily implemented with standard fluorescence microscopes and offers deeper insights into the role of the resting Vm in health and disease.
A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum
Authors: Nakano Michiharu , Hirakawa Hideki , Fukai Eigo , Toyoda Atsushi , Kajitani Rei , Minakuchi Yohei , Itoh Takehiko , Higuchi Yohei , Kozuka Toshiaki , Bono Hidemasa , Shirasawa Kenta , Shiraiwa Ippei , Sumitomo Katsuhiko , Hisamatsu Tamotsu , Shibata Michio , Isobe Sachiko , Taniguchi Kenji , Kusaba Makoto
Published: October 2021

Chrysanthemums are one of the most industrially important cut flowers worldwide. However, their segmental allopolyploidy and self-incompatibility have prevented the application of genetic analysis and modern breeding strategies. We thus developed a model strain, Gojo-0 (Chrysanthemum seticuspe), which is a diploid and self-compatible pure line. Here, we present the 3.05 Gb chromosome-level reference genome sequence, which covered 97% of the C. seticuspe genome. The genome contained more than 80% interspersed repeats, of which retrotransposons accounted for 72%. We identified recent segmental duplication and retrotransposon expansion in C. seticuspe, contributing to arelatively large genome size. Furthermore, we identified a retrotransposon family, SbdRT, which was enriched in gene-dense genome regions and had experienced a very recent transposition burst. We also demonstrated that the chromosome-level genome sequence facilitates positional cloning in C. seticuspe. The genome sequence obtained here can greatly contribute as a reference for chrysanthemum in front-line breeding including genome editing.
Plant-like hooked miniature machines for on-leaf sensing and delivery
Authors: Fiorello Isabella , Meder Fabian , Mondini Alessio , Sinibaldi Edoardo , Filippeschi Carlo , Tricinci Omar , Mazzolai Barbara
Published: October 2021

New sustainable strategies for preserving plants are crucial for tackling environmental challenges. Bioinspired soft and miniature machines have the potential to operate in forests and agricultural fields by adapting their morphology to plant organs like leaves. However, applications on leaf surfaces are limited due to the fragility and heterogeneity of leaves, and harsh outdoor conditions. Here, we exploit the strong shear-dependent leaf-attachment of the hook-climberGalium aparineto create miniature systems that enable precision anchoring to leaf tissues via multifunctional microhooks. We first study the anchoring forces of the microhooks and then fabricate a soft wireless multiparameter sensor to monitor the leaf proximity and degradable hooks forin-plantmolecular delivery to the vascular tissues of the leaves. In addition, we use a soft robotic proof-of-concept demonstrator to highlight how our hooks enable ratchet-like motion on leaves. This research showcases opportunities for specifically designing multifunctional machines for targeted applications in plant ecosystems.
ENSO diversity shows robust decadal variations that must be captured for accurate future projections
Authors: Dieppois Bastien , Capotondi Antonietta , Pohl Benjamin , Chun Kwok Pan , Monerie Paul-Arthur , Eden Jonathan
Published: October 2021

El Niño-Southern Oscillation (ENSO) shows a large diversity of events that is modulated by climate variability and change. The representation of this diversity in climate models limits our ability to predict their impact on ecosystems and human livelihood. Here, we use multiple observational datasets to provide a probabilistic description of historical variations in event location and intensity, and to benchmark models, before examining future system trajectories. We find robust decadal variations in event intensities and locations in century-long observational datasets, which are associated with perturbations in equatorial wind-stress and thermocline depth, as well as extra-tropical anomalies in the North and South Pacific. Some climate models are capable of simulating such decadal variability in ENSO diversity, and the associated large-scale patterns. Projections of ENSO diversity in future climate change scenarios strongly depend on the magnitude of decadal variations, and the ability of climate models to reproduce them realistically over the 21stcentury.
Phytoplankton biodiversity and the inverted paradox
Authors: Behrenfeld Michael J , O’Malley Robert , Boss Emmanuel , Karp-Boss Lee , Mundt Christopher
Published: October 2021

Earth’s aquatic food webs are overwhelmingly supported by planktonic microalgae that live in the sunlit water column where only a minimum number of physical niches are readily identifiable. Despite this paucity of environmental differentiation, these “phytoplankton” populations exhibit a rich biodiversity, an observation not easily reconciled with broadly accepted rules of resource-based competitive exclusion. This conundrum is referred to as the “Paradox of the Plankton”. Consideration of physical distancing between nutrient depletion zones around individual phytoplankton, however, suggests a competition-neutral resource landscape. Application of neutral theory to the sheer number of phytoplankton in physically-mixed water masses yields a prediction of astronomical biodiversity, suggesting the inverted paradox: Why are there so few phytoplankton species? Here, we introduce a trophic constraint on phytoplankton that, when combined with stochastic principals of ecological drift, predicts only modest levels of diversity in an otherwise competition-neutral landscape. Our “trophic exclusion” principle predicts diversity to be independent of population size and yields a species richness across cell-size classes that is consistent with broad oceanographic survey observations.
Probing serum N-glycan patterns for rapid and precise detection of Crohn's disease
Authors: Wu Yonglei , Chen Yijie , Chen Haolin , Yang Chenjie , Shen Xizhong , Deng Chunhui , Sun Nianrong , Wu Hao
Published: October 2021

Serum N-glycan patterns from 50 Crohn‘s disease (CD) patients and 50 healthy controls were acquired by a carbon matrix-based platform. According to statistical analysis, eight specific N-glycans revealed remarkable performance for CD diagnosis.
Progress in controlling the synthesis of atomically precise silver nanoclusters
Authors: He Lizhong , Dong Tingting
Published: October 2021

This short review was designed to summarize the advances in synthesis methods of silver nanoclusters.
Unsupervised machine learning for unbiased chemical classification in X-ray absorption spectroscopy and X-ray emission spectroscopy
Authors: Tetef Samantha , Govind Niranjan , Seidler Gerald T.
Published: October 2021

We utilize unsupervised machine learning to extract chemically relevant information in X-ray absorption near-edge structure (XANES) and in valence-to-core X-ray emission spectra (VtC-XES) for classification of an ensemble of sulphorganic molecules.
Theoretical characterization of zeolite encapsulated platinum clusters in the presence of water molecules
Authors: Bao Qianqian , Zhang Weiwei , Mei Donghai
Published: October 2021

From the DFT calculations, we found the MFI-type zeolite encapsulated Pt metal clusters shows superior stability. The presence of water molecules enhances the interaction between the zeolite framework and the metal clusters, making the configuration more stable.
The joint effect of electrical conductivity and surface oxygen functionalities of carbon supports on the oxygen reduction reaction studied over bare supports and Mn–Co spinel/carbon catalysts in alkaline media
Authors: Kostuch Aldona , Jarczewski Sebastian , Surówka Marcin K. , Kuśtrowski Piotr , Sojka Zbigniew , Kruczała Krzysztof
Published: October 2021

Mn–Co spinel/carbon electrocatalyst performance exhibits a volcano-type shape which results from a trade-off between electrical conductivity and the amount of oxygen groups.
CNC/AgNP hybrids as safer-by-design biocides in paints
Authors: Musino Dafne , Rosset Aurélie , Lelong Cécile , Luche Sylvie , Bergé Virginie , Brochard Grégory , Plumail Manon , Trouiller Benedicte , Auger Aurélien , Guiot Arnaud , Patouillard Julien , Desrousseaux Stephanie , Artous Sébastien , Rabilloud Thierry , Boutry Delphine , Capron Isabelle
Published: October 2021

An efficient biocidal paint is prepared. Antibacterial activity is provided by silver nanoparticles (AgNPs) nucleated on a bio-based substrate (cellulose nanocrystals, CNCs), dispersed in an amount as low as possible in aqueous suspension.
Formation sequence of solid electrolyte interphases and impacts on lithium deposition and dissolution on copper: an in situ atomic force microscopic study
Authors: Wang Wei-Wei , Gu Yu , Yan Hao , Li Kai-Xuan , Chen Zhao-Bin , Wu Qi-Hui , Kranz Christine , Yan Jia-Wei , Mao Bing-Wei
Published: October 2021

In situ AFM monitoring of the morphology evolution of Li deposits reveals that SEIs could be more influential on Li dissolution, and spatial integration of the SEI shell on Li deposits is important to maintain reversible deposition and dissolution cycles.
Interrogating the transcriptome with metabolically incorporated ribonucleosides
Authors: Kleiner Ralph E.
Published: October 2021

This review summarizes recent developments in metabolic labeling of RNA to study RNA synthesis and turnover, RNA binding proteins, and RNA modifications and modifying enzymes.
Catalytic oxidation of high-concentration CO over La0.9M0.1CoO3 (M = Ce, Sr) facilely promoted by glucose
Authors: Teng Zihao , Yun Jianyu , Du Libin , Huang Junqin , Hao Qinglan , Dou Baojuan , Hui Kwun Nam , Bin Feng
Published: October 2021

Addition of glucose and introduction of Ce/Sr into LaCoO3 can create more oxygen vacancies and Co3+ active sites, facilitating the catalytic activity for CO oxidation.
The Dirac cone in two-dimensional tetragonal silicon carbides: a ring coupling mechanism
Authors: Kong Weixiang , Xiao Xiaoliang , Xu Wangping , Wang Rui , Gan Li-Yong , Wei Juan , Fan Jing , Wu Xiaozhi
Published: October 2021

The exploration of novel two-dimensional semimetallic materials is always an attractive topic.
Application of a super-stretched self-healing elastomer based on methyl vinyl silicone rubber for wearable electronic sensors
Authors: Yu Tianwen , Shan Yifei , Li Zhixi , Wang Xiaoxiao , Cui Huanan , Yang Kun , Cui Yongyan
Published: October 2021

A super-stretched self-healing elastomer for flexible electronic devices by introducing quadruple hydrogen bonds.
Electrochemical reduction of nitrate to ammonia in a fluidized electrocatalysis system with oxygen vacancy-rich CuOx nanoparticles
Authors: Geng Jing , Ji Sihan , Xu Hui , Zhao Cuijiao , Zhang Shengbo , Zhang Haimin
Published: October 2021

A fluidized electrocatalysis system utilizing oxygen vacancy rich CuOX nanoparticle catalysts in an electrolyte was developed to achieve a high NH3 yield rate and faradaic efficiency through the electrocatalytic nitrate reduction reaction.
Hydroxyl group-directed, tartaric acid-catalyzed synthesis of meta-functionalized aryl ethers and phenols through domino conjugate addition/aromatization of para-quinols
Authors: Chen Guo-Shu , Li Jia-Hui , Chen Shu-Jie , Lin Wen-Xia , Ren Hai , Deng Dong-Sheng , Liu Yun-Lin
Published: October 2021

A tartaric acid-catalyzed three-component reaction of para-quinols, organoboronic acids, and alcohols affords meta-alkenylated aryl alkyl ether in good yields. In the absence of alcohols, meta-functionalized phenols could be obtained selectively.
Rh(iii)-Catalyzed tandem C(sp2)–H allylation/N-alkylation annulation of arene amides with 2-alkylidenetrimethylene carbonates
Authors: Xie Hui , Liang Jin-Yi , Huang Zhuo-Jun , Shu Bing , Zheng Yi-Chuan , Liu Yan-Zhi , Chen Shao-Yong , Liu Xu-Ge , Zhang Shang-Shi
Published: October 2021

A Rh(iii)-catalyzed tandem C(sp2)–H allylation/N-alkylation annulation reaction of arene amides employing 5-methylene-1,3-dioxan-2-one as an efficient allyl source has been disclosed for the first time.
FeII4L4 tetrahedron binds and aggregates DNA G-quadruplexes
Authors: Zhu Jinbo , Yan Zhiqiang , Bošković Filip , Haynes Cally J. E. , Kieffer Marion , Greenfield Jake L. , Wang Jin , Nitschke Jonathan R. , Keyser Ulrich F.
Published: October 2021

We find FeII4L4 binds to G-quadruplex and forms aggregates. G-quadruplex in the aggregates is protected from digestion by S1 nuclease.
Analysis of H2O-induced surface degradation in SrCoO3-derivatives and its impact on redox kinetics
Authors: Cavallaro Andrea , Wilson George E. , Kerherve Gwilherm , Cali Eleonora , van den Bosch Celeste A. M. , Boldrin Paul , Payne David , Skinner Stephen J. , Aguadero Ainara
Published: October 2021

Substituted SrCoO3 surface decomposition in contact with water and its effect on the cathode redox kinetics.
Biomimetic and immunomodulatory baicalin-loaded graphene oxide-demineralized bone matrix scaffold for in vivo bone regeneration
Authors: Guo Bing , Feng Xiaodong , Wang Yun , Wang Xiansong , He Yue
Published: October 2021

A bifunctional GO–BAI/DBM scaffold with enhanced osteoinductive and immunomodulatory performance significantly enhanced material-mediated osteogenesis and angiogenesis via the coordinated involvement of macrophages and bone mesenchymal stem cells.
Interfacial design of gold/silver core–shell nanostars for plasmon-enhanced photocatalytic coupling of 4-aminothiophenol
Authors: Kaur Gagandeep , Tanwar Swati , Kaur Vishaldeep , Biswas Rathindranath , Saini Sangeeta , Haldar Krishna Kanta , Sen Tapasi
Published: October 2021

An interfacial designing procedure is presented for the fabrication of bimetallic hybrid nanomaterials to serve as highly efficient SERS substrate and plasmon driven catalyst for dimerization reaction of PATP utilizing Au/Ag core–shell nanostars.
Boron dopant simultaneously achieving nanostructure control and electronic structure tuning of graphitic carbon nitride with enhanced photocatalytic activity
Authors: Wang Xin , Liu Boyan , Xiao Xiong , Wang Songcan , Huang Wei
Published: October 2021

The boron-doped graphitic carbon nitride synthesized by two-step heat treatment has a one-dimensional tubular structure and its hydrogen evolution is 2 times higher than that of undoped g-C3N4.
Complex multitask compressive sensing using Laplace priors
Authors: Zhang Qilei , Dong Zhen , Zhang Yongsheng
Published: October 2021

Most existing Bayesian compressive sensing (BCS) algorithms are developed in real numbers. This results in many difficulties in applying BCS to solve complex‐valued problems. To overcome this limitation, this letter extends the existing real‐valued BCS framework to the complex‐valued BCS framework. Within this framework, the multitask learning setting, where L tasks are statistically interrelated and share the same prior, is considered. It is verified by numerical examples that the developed complex multitask compressive sensing (CMCS) algorithm is more accurate and effective than the existing algorithms for the complex sparse signal reconstructions
Charge vibration behaviour in polyimide under the pulse voltage with different rise and fall times
Authors: Zhang Tao , He Dongxin , Wei Junyu , Liu Hongshun , Li Qingquan , Teyssedre Gilbert
Published: October 2021

High‐voltage electronic equipment is widely used in power systems, which normally operate under the pulse voltage condition. However, compared to DC or AC stress, the electrical insulation suffers a more severe ageing process under a pulse voltage with steep edges and so may cause electrical equipments to fail early. The charge behaviour in polyimide under the pulse voltage with different edge times was investigated in this study. The experimental results show that charges vibrate at the pulse edge, while the amplitude of charge vibration increases with decreasing edge times. Furthermore, the detected vibration signal is strong within the nanosecond edge times, while being negligible in the microsecond range. Notably, the amplitude of charge vibration at the falling edge is larger than that at the rising edge in the presence of the column‐plate electrode. It is believed that the resultant force acting on the charge increases drastically at the pulse edges, leading to the charge movement and the generation of ultrasonic waves, with the resultant force becoming larger when the edge times decrease. Charge vibration behaviour is harmful to the microstructure of insulation materials, and so it may be concluded that the rise and fall times of the pulse voltage play an important role in insulation failure.