bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained productivity and agronomic potential of perennial rice
Authors: Zhang Shilai , Huang Guangfu , Zhang Yujiao , Lv Xiutao , Wan Kejiang , Liang Jian , Feng Yupeng , Dao Jinrong , Wu Shukang , Zhang Lin , Yang Xu , Lian Xiaoping , Huang Liyu , Shao Lin , Zhang Jing , Qin Shiwen , Tao Dayun , Crews Timothy E. , Sacks Erik J. , Lyu Jun , Wade Len J. , Hu Fengyi 
Published: November 2022

AbstractThere is an urgent need for agricultural systems to intensify sustainably, increasing crop productivity, farmer livelihoods and soil health while using fewer resources. Crop perennialization, the conversion of especially annual grains to perennial forms, has shown such possibility. Here we report the successful breeding of perennial rice and assess its performance and potential. Domesticated, annual Asian rice (Oryza sativa) was hybridized with its perennial African relative Oryza longistaminata. From a single planting, irrigated perennial rice produced grain for eight consecutive harvests over four years, averaging 6.8 Mg ha−1 harvest−1 versus the 6.7 Mg of replanted annual rice, which required additional labour and seed. Four years of cropping with perennial rice resulted in soils accumulating 0.95 Mg ha–1 yr–1 organic carbon and 0.11 Mg ha−1 yr−1 nitrogen, along with increases in soil pH (0.3–0.4) and plant-available water capacity (7.2 mm). Perennial cultivars are strongly preferred by farmers; growing them saves 58.1% of labour and 49.2% of input costs in each regrowth cycle. In 2021, perennial rice was grown on 15,333 ha by 44,752 smallholder farmers in southern China. Suited to a broad range of frost-free environments between 40° N and 40° S, perennial rice is a step change with potential to improve livelihoods, enhance soil quality and inspire research on other perennial grains.
Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese
Authors: Ouyang Jing , Zheng Sumei , Huang Min , Tang Hongbo , Qiu Xiaohui , Chen Shoujin , Wang Zhangzhang , Zhou Zhongdong , Gao Yuren , Xiong Yanpeng , Zeng Guohua , Huang Jimin , He Jiugen , Ren Jun , Chen Hao , Yan Xueming 
Published: November 2022

AbstractGeese are herbivorous birds that play an essential role in the agricultural economy. We construct the chromosome-level genome of a Chinese indigenous goose (the Xingguo gray goose, XGG; Anser cygnoides) and analyze the adaptation of fat storage capacity in the goose liver during the evolution of Anatidae. Genomic resequencing of 994 geese is used to investigate the genetic relationships of geese, which supports the dual origin of geese (Anser cygnoides and Anser anser). Chinese indigenous geese show higher genetic diversity than European geese, and a scientific conservation program can be established to preserve genetic variation for each breed. We also find that a 14-bp insertion in endothelin receptor B subtype 2 (EDNRB2) that determines the white plumage of Chinese domestic geese is a natural mutation, and the linkaged alleles rapidly increase in frequency as a result of genetic hitchhiking, leading to the formation of completely different haplotypes of white geese under strong artificial selection. These genomic resources and our findings will facilitate marker-assisted breeding of geese and provide a foundation for further research on geese genetics and evolution.
A substrate-induced gating mechanism is conserved among Gram-positive IgA1 metalloproteases
Authors: Redzic Jasmina S. , Rahkola Jeremy , Tran Norman , Holyoak Todd , Lee Eunjeong , Martín-Galiano Antonio Javier , Meyer Nancy , Zheng Hongjin , Eisenmesser Elan 
Published: November 2022

AbstractThe mucosal adaptive immune response is dependent on the production of IgA antibodies and particularly IgA1, yet opportunistic bacteria have evolved mechanisms to specifically block this response by producing IgA1 proteases (IgA1Ps). Our lab was the first to describe the structures of a metal-dependent IgA1P (metallo-IgA1P) produced from Gram-positive Streptococcus pneumoniae both in the absence and presence of its IgA1 substrate through cryo-EM single particle reconstructions. This prior study revealed an active-site gating mechanism reliant on substrate-induced conformational changes to the enzyme that begged the question of whether such a mechanism is conserved among the wider Gram-positive metallo-IgA1P subfamily of virulence factors. Here, we used cryo-EM to characterize the metallo-IgA1P of a more distantly related family member from Gemella haemolysans, an emerging opportunistic pathogen implicated in meningitis, endocarditis, and more recently bacteremia in the elderly. While the substrate-free structures of these two metallo-IgA1Ps exhibit differences in the relative starting positions of the domain responsible for gating substrate, the enzymes have similar domain orientations when bound to IgA1. Together with biochemical studies that indicate these metallo-IgA1Ps have similar binding affinities and activities, these data indicate that metallo-IgA1P binding requires the specific IgA1 substrate to open the enzymes for access to their active site and thus, largely conform to an “induced fit” model.
Topological bulk solitons in a nonlinear photonic Chern insulator
Authors: Li Rujiang , Kong Xiangyu , Hang Dongkai , Li Guoyi , Hu Hongyu , Zhou Hao , Jia Yongtao , Li Pengfei , Liu Ying 
Published: November 2022

AbstractNonlinearities in lattices with topological band structures can induce topological interfaces in the bulk of structures and give rise to bulk solitons in the topological bandgaps. Here we study a photonic Chern insulator with saturable nonlinearity and show the existence of topological bulk solitons. The fundamental bulk solitons exhibit as semi-vortex solitons, where only one pseudospin component has a nonzero vorticity. The bulk solitons have equal angular momentum at different valleys. This phenomenon is a direct outcome of the topology of the linear host lattice and the angular momentum can be changed by switching the sign of the nonlinearity. The bulk solitons bifurcate from the linear bulk band edge and terminate when their powers saturate. We find that these bulk solitons are stable within the whole spectrum range. Moreover, these bulk solitons are robust against lattice disorders both from on-site energies and hopping amplitudes. Our work extends the study of Chern insulators into the nonlinear regime and highlights the interplay between topology and nonlinearity.
Dynamic spatio-temporal control of naturally sourced soft photonic crystals
Authors: Guidetti Giulia , Pirie Chris , Matzeu Giusy , Bonacchini Giorgio E. , Kim Beom Joon , Napier Bradley , Omenetto Fiorenzo G. 
Published: November 2022

AbstractThe quest for flexible curvilinear displays is driving renewed interest in natural soft photonic systems that rely on the adaptable response of nanostructured living tissues to external stimuli for camouflage and energy management. Understanding and controlling the dynamics of these systems is challenging due to difficulties in sourcing the tissues and constraints in the ability to stimulate them. Here, we present an ex-vivo approach to systematically investigate soft biophotonic crystals and dynamically control their response by using the Bos taurus tapetum as a model system. The tapetum’s structural color is controlled chemically and electronically and examined by multispectral imaging providing insights on the color change dynamics. The ability to spatio-temporally control the optical response of biophotonic crystals provides insights for the development of soft photonic systems for displays and dynamic light management.
Global patterns and predictors of C:N:P in marine ecosystems
Authors: Tanioka Tatsuro , Garcia Catherine A. , Larkin Alyse A. , Garcia Nathan S. , Fagan Adam J. , Martiny Adam C. 
Published: November 2022

AbstractOceanic nutrient cycles are coupled, yet carbon-nitrogen-phosphorus (C:N:P) stoichiometry in marine ecosystems is variable through space and time, with no clear consensus on the controls on variability. Here, we analyze hydrographic, plankton genomic diversity, and particulate organic matter data from 1970 stations sampled during a global ocean observation program (Bio-GO-SHIP) to investigate the biogeography of surface ocean particulate organic matter stoichiometry. We find latitudinal variability in C:N:P stoichiometry, with surface temperature and macronutrient availability as strong predictors of stoichiometry at high latitudes. Genomic observations indicated community nutrient stress and suggested that nutrient supply rate and nitrogen-versus-phosphorus stress are predictive of hemispheric and regional variations in stoichiometry. Our data-derived statistical model suggests that C:P and N:P ratios will increase at high latitudes in the future, however, changes at low latitudes are uncertain. Our findings suggest systematic regulation of elemental stoichiometry among ocean ecosystems, but that future changes remain highly uncertain.
TbasCO: trait-based comparative ‘omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome
Authors: McDaniel E A , van Steenbrugge J J M , Noguera D R , McMahon K D , Raaijmakers J M , Medema M H , Oyserman B O 
Published: November 2022

Abstract
A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.
Basal Cell Carcinoma of the Head and Neck—A Retrospective Single-Centre Comparison of the Recurrence Rate after R0 or R1 Resection
Authors: Stankovic Petar , Bock Robert , Rudhart Stefan A. , Hoch Stephan , Wilhelm Thomas 
Published: November 2022

AbstractThe treatment guidelines for basal cell carcinoma (BCC) postulate complete surgical excision using microscopically controlled resection (MOHS) as the gold standard. The need to obtain a small safety margin in the complex anatomical area of the head and neck is very challenging due to the individual characteristics (localization, histology, and size) of tumors and the fact that the postoperative loss of quality of life depends on the surgical defect size. The R1 status is histopathologically defined when the safety margin is less than 1 mm even if there are no tumor cells actually infiltrating the resection margin. Therefore, some studies have already favored a watch-and-wait-strategy in R1 situations. We aimed to evaluate the outcome and recurrence rate of resected BCCs of the head and neck, especially in a histologically proven R1 situation. The outcomes of all resected BCCs observed during a 5-year period (January 2009–December 2013) in a tertiary care center were analyzed. Our standard operating procedure was microscopically controlled surgical excision with reresections until an R0 situation was achieved. In selected patients, an R1 status has been accepted after at least two resections. From the included 191 BCCs, the R1 status was accepted as the final result in 46 (24.1%) cases which had surgically clear margins and were closely followed-up. From 54 patients in the R0 and 40 patients in the R1 group who completed the follow-up (2.4 ± 0.4 years), we observed 0 and 2 local recurrences, respectively (p = 0.19). In cases where frequent follow-up can be secured and the surgical area is delicate, a surgical closure at R1 status can be justified as the recurrence rate is not significantly higher compared with R0.
Assessment of Efficacy and Adverse Effects of Bismuth-Based Treatment Combined with Bifidobacterium Lactis for Eradication of Helicobacter Pylori in Turkish Children
Authors: Bolat Ahmet , Yaprak Deniz , Arslan Melike , Büyükcam Ayşe , Balamtekin Necati 
Published: November 2022

AbstractObjective There are many adverse effects of drugs used to eradicate Helicobacter pylori, and reconstructing the microbiota by external ingestion of probiotics seems to have good effects on H. pylori eradication and prevents side effects.Methods The study included 161 outpatients aged between 8 and 18 years diagnosed with H. pylori gastritis in the Gülhane Training and Research Hospital Pediatric Gastroenterology unit from June 1, 2018, through March 31, 2020, and patients were randomized into two groups. Eighty patients in the probiotic group (first group) received H. pylori eradication therapy for 14 days; additionally, Bifidobacterium lactis B94 was administered for 14 days for eradication of H. pylori. Eighty-one patients in the standard therapy group (second group) received the same eradication therapy but no probiotics. All patients were asked to complete a detailed questionnaire regularly, including changes in symptoms and side effects of drugs on days 0, 7, and 14 of treatment. The eradication success was checked with the H. pylori stool antigen test kit 8 weeks after completion of the treatment regimen.Results The mean age of the patients was 14.2 ± 2.9 years, and 88 (64.7%) were female. The eradication rates were similar between the standard therapy and the probiotic groups by intention-to-treat analysis (p = 0.930). In order of frequency, the most common eradication treatment–related side effects were abdominal pain, taste abnormalities, and anorexia. In addition, therapy-related epigastric pain and flatulence were similar initially (p > 0.05) but seemed to be significantly lower in the probiotic group than in the standard therapy group on days 7 and 14 (p < 0.05).Conclusions Our results suggest that additional probiotic supplementation has not changed the eradication rates but seems to reduce some specific gastrointestinal adverse events in children with H. pylori infections treated with a bismuth-based quadruple eradication regimen. More extensive randomized controlled trials are needed to explain probiotics' effects on H. pylori eradication and drug side effects.
High-fidelity inference of local impurity profiles in C-2W using Bayesian tomography
Authors: Nations M. , Romero J. A. , Gupta D. K. , Sweeney J. ,   the TAE Team
Published: November 2022

In C-2W (also called “Norman”) [1], beam-driven field reversed configuration plasmas embedded in a magnetic mirror are produced and sustained in a steady state. A multi-chord passive Doppler spectroscopy diagnostic provides line-integrated impurity emission measurements near the center plane of the confinement vessel with fast time resolution. The high degree of plasma non-uniformity across optical sightlines can preclude direct fitting of the measured line-integrated spectra. To overcome this challenge, local impurity profiles are inferred using Bayesian tomography, a superior analysis technique based on a complete forward model of the diagnostic. The measured emission of O4+ triplet lines near 278.4 nm is modeled assuming two independent populations: thermal and beam ions. Gaussian processes are used to generate and infer local profiles. The inference incorporates details of the geometrical arrangement of the diagnostic, instrument function, intensity calibration, and a noise model. Markov chain Monte Carlo (MCMC) sampling of the posterior distribution of solutions provides high-fidelity uncertainty estimates. The reconstructed O4+ impurity profiles are consistent with data from other diagnostics and show good agreement with expected physics based on previously developed models of biasing circuit and impurity transport.
First magnifying neutron/x-ray combined radiography at Shenguang laser facility
Authors: Li J. J. , Yu B. , Xu T. , Chen Z. J. , Zheng J. H. , Yao L. , Dong Y. S. , Yang J. M. 
Published: November 2022

Neutron/x-ray combined radiography can integrate the merits of x-ray and neutron radiography and have an enhanced non-destructive detecting capability compared to single neutron or x-ray radiography. In this work, magnifying neutron/x-ray combined radiography along the same line of sight was performed at the Shenguang (SG) laser facility for the first time. Based on ∼0.1 mm point-like backlight sources of neutrons and x rays, structural defects on the order of ∼0.2 mm within polyethylene and Fe were observed in neutron and x-ray radiography, respectively. In addition, the spatial resolution obtained was 0.68 ∼ 2.05 mm in the object position for neutron radiography and ∼0.14 mm for x-ray radiography. This indicated that the combined radiography system arranged along the same line of sight at the SG laser facility possessed the ability to inspect structural defects within both low-Z and high-Z materials simultaneously, with relatively high spatial resolution.
Modes of Pangean lake level cyclicity driven by astronomical climate pacing modulated by continental position and
p
CO2
Authors: Landwehrs Jan , Feulner Georg , Willeit Matteo , Petri Stefan , Sames Benjamin , Wagreich Michael , Whiteside Jessica H. , Olsen Paul E. 
Published: November 2022

Orbital cyclicity is a fundamental pacemaker of Earth’s climate system. The Newark–Hartford Basin (NHB) lake sediment record of eastern North America contains compelling geologic expressions of this cyclicity, reflecting variations of climatic conditions in tropical Pangea during the Late Triassic and earliest Jurassic (~233 to 199 Ma). Climate modeling enables a deeper mechanistic understanding of Earth system modulation during this unique greenhouse and supercontinent period. We link major features of the NHB record to the combined climatic effects of orbital forcing, paleogeographic changes, and atmospheric
p
CO

2

variations. An ensemble of transient, orbitally driven climate simulations is assessed for nine time slices, three atmospheric
p
CO

2

values, and two paleogeographic reconstructions. Climatic transitions from tropical humid to more seasonal and ultimately semiarid are associated with tectonic drift of the NHB from

~
5

°

N

to

20

°

N

. The modeled orbital modulation of the precipitation–evaporation balance is most pronounced during the 220 to 200 Ma interval, whereas it is limited by weak seasonality and increasing aridity before and after this interval. Lower
p
CO

2

at around 205 Ma contributes to drier climates and could have led to the observed damping of sediment cyclicity. Eccentricity-modulated precession dominates the orbitally driven climate response in the NHB region. High obliquity further amplifies summer precipitation through the seasonal shifts in the tropical rainfall belt. Regions with other proxy records are also assessed, providing guidance toward an integrated picture of global astronomical climate forcing in the Late Triassic and ultimately of other periods in Earth history.
Environmental drivers of the first major animal extinction across the Ediacaran White Sea-Nama transition
Authors: Evans Scott D. , Tu Chenyi , Rizzo Adriana , Surprenant Rachel L. , Boan Phillip C. , McCandless Heather , Marshall Nathan , Xiao Shuhai , Droser Mary L. 
Published: November 2022

The Ediacara Biota—the oldest communities of complex, macroscopic fossils—consists of three temporally distinct assemblages: the Avalon (ca. 575–560 Ma), White Sea (ca. 560–550 Ma), and Nama (ca. 550–539 Ma). Generic diversity varies among assemblages, with a notable decline at the transition from White Sea to Nama. Preservation and sampling biases, biotic replacement, and environmental perturbation have been proposed as potential mechanisms for this drop in diversity. Here, we compile a global database of the Ediacara Biota, specifically targeting taphonomic and paleoecological characters, to test these hypotheses. Major ecological shifts in feeding mode, life habit, and tiering level accompany an increase in generic richness between the Avalon and White Sea assemblages. We find that ∼80% of White Sea taxa are absent from the Nama interval, comparable to loss during Phanerozoic mass extinctions. The paleolatitudes, depositional environments, and preservational modes that characterize the White Sea assemblage are well represented in the Nama, indicating that this decline is not the result of sampling bias. Counter to expectations of the biotic replacement model, there are minimal ecological differences between these two assemblages. However, taxa that disappear exhibit a variety of morphological and behavioral characters consistent with an environmentally driven extinction event. The preferential survival of taxa with high surface area relative to volume may suggest that this was related to reduced global oceanic oxygen availability. Thus, our data support a link between Ediacaran biotic turnover and environmental change, similar to other major mass extinctions in the geologic record.
Switchable targeting of solid tumors by BsCAR T cells
Authors: Stepanov Alexey V. , Kalinin Roman S. , Shipunova Victoria O. , Zhang Ding , Xie Jia , Rubtsov Yuri P. , Ukrainskaya Valeria M. , Schulga Alexey , Konovalova Elena V. , Volkov Dmitry V. , Yaroshevich Igor A. , Moysenovich Anastasiia M. , Belogurov Alexey A. , Zhang Hongkai , Telegin Georgij B. , Chernov Alexandr S. , Maschan Mikhail A. , Terekhov Stanislav S. , Wu Peng , Deyev Sergey M. , Lerner Richard A. , Gabibov Alexander G. , Altman Sidney 
Published: November 2022

The development of chimeric antigen receptor (CAR) T cell therapy has become a critical milestone in modern oncotherapy. Despite the remarkable in vitro effectiveness, the problem of safety and efficacy of CAR T cell therapy against solid tumors is challenged by the lack of tumor-specific antigens required to avoid on-target off-tumor effects. Spatially separating the cytotoxic function of CAR T cells from tumor antigen recognition provided by protein mediators allows for the precise control of CAR T cell cytotoxicity. Here, the high affinity and capability of the bacterial toxin-antitoxin barnase-barstar system were adopted to guide CAR T cells to solid tumors. The complementary modules based on (
1
) ankyrin repeat (DARPin)-barnase proteins and (
2
) barstar-based CAR (BsCAR) were designed to provide switchable targeting to tumor cells. The alteration of the DARPin-barnase switches enabled the targeting of different tumor antigens with a single BsCAR. A gradual increase in cytokine release and tunable BsCAR T cell cytotoxicity was achieved by varying DARPin-barnase loads. Switchable BsCAR T cell therapy was able to eradicate the HER2
+
ductal carcinoma in vivo. Guiding BsCAR T cells by DARPin-barnase switches provides a universal approach for a controlled multitargeted adoptive immunotherapy.