bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of inquiries on weed control efficacy of XtendiMax® herbicide with VaporGrip® technology
Authors: Varanasi Aruna , Singh Daljit , Krebel Jenny , Herrmann Jeffrey , Willis John , Elmore Greg , Fischer Joshua , Witten Ty , Head Graham , Aradhya Chandrashekar 
Published: November 2023

AbstractHerbicide resistance in weeds significantly threatens crop production in the United States. The introduction of dicamba-resistant soybean and cotton stacked with other herbicide tolerance traits has provided farmers with the flexibility of having multiple herbicide options to diversify their weed management practices and delay resistance evolution. XtendiMax® herbicide with VaporGrip® Technology is a dicamba formulation registered for use on dicamba-resistant soybean and cotton crops by the U.S. Environmental Protection Agency (EPA). One of the terms of its registration includes an evaluation of inquiries on reduced weed control efficacy by growers or users of XtendiMax for suspected weed resistance. A total of 3,555 product performance inquiries (PPIs) were received from 2018 to 2021 regarding reduced weed control efficacy by dicamba. Following the criteria recommended by EPA for screening of suspected resistance in the field, a total of 103 weed accessions from 63 counties in 13 states were collected for greenhouse testing over those 4 yr. Weed accessions for greenhouse testing were collected only in states where resistance to dicamba was not yet confirmed in the weed species under investigation. The accessions, which consisted primarily of waterhemp and Palmer amaranth, were treated with dicamba at rates of 560 g ae ha−1 and 1,120 g ae ha−1. All weed accessions, except for one accession each of Palmer amaranth and waterhemp, were controlled by ≥90% with dicamba at 21 d after treatment in the greenhouse.
30×30 biodiversity gains rely on national coordination
Authors: Eckert Isaac , Brown Andrea , Caron Dominique , Riva Federico , Pollock Laura J. 
Published: November 2023

AbstractGlobal commitments to protect 30% of land by 2030 present an opportunity to combat the biodiversity crisis, but reducing extinction risk will depend on where countries expand protection. Here, we explore a range of 30×30 conservation scenarios that vary what dimension of biodiversity is prioritized (taxonomic groups, species-at-risk, biodiversity facets) and how protection is coordinated (transnational, national, or regional approaches) to test which decisions influence our ability to capture biodiversity in spatial planning. Using Canada as a model nation, we evaluate how well each scenario captures biodiversity using scalable indicators while accounting for climate change, data bias, and uncertainty. We find that only 15% of all terrestrial vertebrates, plants, and butterflies (representing only 6.6% of species-at-risk) are adequately represented in existing protected land. However, a nationally coordinated approach to 30×30 could protect 65% of all species representing 40% of all species-at-risk. How protection is coordinated has the largest impact, with regional approaches protecting up to 38% fewer species and 65% fewer species-at-risk, while the choice of biodiversity incurs much smaller trade-offs. These results demonstrate the potential of 30×30 while highlighting the critical importance of biodiversity-informed national strategies.
Enzymatic β-elimination in natural product O- and C-glycoside deglycosylation
Authors: Bitter Johannes , Pfeiffer Martin , Borg Annika J. E. , Kuhlmann Kirill , Pavkov-Keller Tea , Sánchez-Murcia Pedro A. , Nidetzky Bernd 
Published: November 2023

AbstractBiological degradation of natural product glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, we discover an O-glycoside β-eliminase (OGE) from Agrobacterium tumefaciens that converts the C3-oxidized O-β-d-glucoside of phloretin (a plant-derived flavonoid) into the aglycone and the 2-hydroxy-3-keto-glycal elimination product. While unrelated in sequence, OGE is structurally homologous to, and shows effectively the same Mn2+ active site as, the C-glycoside deglycosylating enzyme (CGE) from a human intestinal bacterium implicated in β-elimination of 3-keto C-β-d-glucosides. We show that CGE catalyzes β-elimination of 3-keto O- and C-β-d-glucosides while OGE is specific for the O-glycoside substrate. Substrate comparisons and mutagenesis for CGE uncover positioning of aglycone for protonic assistance by the enzyme as critically important for C-glycoside cleavage. Collectively, our study suggests convergent evolution of active site for β-elimination of 3-keto O-β-d-glucosides. C-Glycoside cleavage is a specialized feature of this active site which is elicited by substrate through finely tuned enzyme-aglycone interactions.
Covariance patterns between sleep health domains and distributed intrinsic functional connectivity
Authors: Wang Yulin , Genon Sarah , Dong Debo , Zhou Feng , Li Chenyu , Yu Dahua , Yuan Kai , He Qinghua , Qiu Jiang , Feng Tingyong , Chen Hong , Lei Xu 
Published: November 2023

AbstractSleep health is both conceptually and operationally a composite concept containing multiple domains of sleep. In line with this, high dependence and interaction across different domains of sleep health encourage a transition in sleep health research from categorical to dimensional approaches that integrate neuroscience and sleep health. Here, we seek to identify the covariance patterns between multiple sleep health domains and distributed intrinsic functional connectivity by applying a multivariate approach (partial least squares). This multivariate analysis reveals a composite sleep health dimension co-varying with connectivity patterns involving the attentional and thalamic networks and which appear relevant at the neuromolecular level. These findings are further replicated and generalized to several unseen independent datasets. Critically, the identified sleep-health related connectome shows diagnostic potential for insomnia disorder. These results together delineate a potential brain connectome biomarker for sleep health with high potential for clinical translation.
In situ imaging of the atomic phase transition dynamics in metal halide perovskites
Authors: Ma Mengmeng , Zhang Xuliang , Chen Xiao , Xiong Hao , Xu Liang , Cheng Tao , Yuan Jianyu , Wei Fei , Shen Boyuan 
Published: November 2023

AbstractPhase transition dynamics are an important concern in the wide applications of metal halide perovskites, which fundamentally determine the optoelectronic properties and stabilities of perovskite materials and devices. However, a more in-depth understanding of such a phase transition process with real atomic resolution is still limited by the immature low-dose electron microscopy and in situ imaging studies to date. Here, we apply an emergent low-dose imaging technique to identify different phase structures (α, β and γ) in CsPbI3 nanocrystals during an in-situ heating process. The rotation angles of PbI6 octahedrons can be measured in these images to quantitatively describe the thermal-induced phase distribution and phase transition. Then, the dynamics of such a phase transition are studied at a macro time scale by continuously imaging the phase distribution in a single nanocrystal. The structural evolution process of CsPbI3 nanocrystals at the particle level, including the changes in morphology and composition, is also visualized with increasing temperature. These results provide atomic insights into the transition dynamics of perovskite phases, indicating a long-time transition process with obvious intermediate states and spatial distribution that should be generally considered in the further study of structure-property relations and device performance.
GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers
Authors: Ravid Lustig Liat , Sampath Kumar Abhishek , Schwämmle Till , Dunkel Ilona , Noviello Gemma , Limberg Elodie , Weigert Raha , Pacini Guido , Buschow René , Ghauri Afrah , Stötzel Maximilian , Wittler Lars , Meissner Alexander , Schulz Edda G. 
Published: November 2023

AbstractX-chromosome inactivation (XCI) balances gene expression between the sexes in female mammals. Shortly after fertilization, upregulation of Xist RNA from one X chromosome initiates XCI, leading to chromosome-wide gene silencing. XCI is maintained in all cell types, except the germ line and the pluripotent state where XCI is reversed. The mechanisms triggering Xist upregulation have remained elusive. Here we identify GATA transcription factors as potent activators of Xist. Through a pooled CRISPR activation screen in murine embryonic stem cells, we demonstrate that GATA1, as well as other GATA transcription factors can drive ectopic Xist expression. Moreover, we describe GATA-responsive regulatory elements in the Xist locus bound by different GATA factors. Finally, we show that GATA factors are essential for XCI induction in mouse preimplantation embryos. Deletion of GATA1/4/6 or GATA-responsive Xist enhancers in mouse zygotes effectively prevents Xist upregulation. We propose that the activity or complete absence of various GATA family members controls initial Xist upregulation, XCI maintenance in extra-embryonic lineages and XCI reversal in the epiblast.
Biosynthesis of natural and halogenated plant monoterpene indole alkaloids in yeast
Authors: Bradley Samuel A. , Lehka Beata J. , Hansson Frederik G. , Adhikari Khem B. , Rago Daniela , Rubaszka Paulina , Haidar Ahmad K. , Chen Ling , Hansen Lea G. , Gudich Olga , Giannakou Konstantina , Lengger Bettina , Gill Ryan T. , Nakamura Yoko , de Bernonville Thomas Dugé , Koudounas Konstantinos , Romero-Suarez David , Ding Ling , Qiao Yijun , Frimurer Thomas M. , Petersen Anja A. , Besseau Sébastien , Kumar Sandeep , Gautron Nicolas , Melin Celine , Marc Jillian , Jeanneau Remi , O’Connor Sarah E. , Courdavault Vincent , Keasling Jay D. , Zhang Jie , Jensen Michael K. 
Published: November 2023

AbstractMonoterpenoid indole alkaloids (MIAs) represent a large class of plant natural products with marketed pharmaceutical activities against a wide range of indications, including cancer, malaria and hypertension. Halogenated MIAs have shown improved pharmaceutical properties; however, synthesis of new-to-nature halogenated MIAs remains a challenge. Here we demonstrate a platform for de novo biosynthesis of two MIAs, serpentine and alstonine, in baker’s yeast Saccharomyces cerevisiae and deploy it to systematically explore the biocatalytic potential of refactored MIA pathways for the production of halogenated MIAs. From this, we demonstrate conversion of individual haloindole derivatives to a total of 19 different new-to-nature haloserpentine and haloalstonine analogs. Furthermore, by process optimization and heterologous expression of a modified halogenase in the microbial MIA platform, we document de novo halogenation and biosynthesis of chloroalstonine. Together, this study highlights a microbial platform for enzymatic exploration and production of complex natural and new-to-nature MIAs with therapeutic potential.
sciCSR infers B cell state transition and predicts class-switch recombination dynamics using single-cell transcriptomic data
Authors: Ng Joseph C. F. , Montamat Garcia Guillem , Stewart Alexander T. , Blair Paul , Mauri Claudia , Dunn-Walters Deborah K. , Fraternali Franca 
Published: November 2023

AbstractClass-switch recombination (CSR) is an integral part of B cell maturation. Here we present sciCSR (pronounced ‘scissor’, single-cell inference of class-switch recombination), a computational pipeline that analyzes CSR events and dynamics of B cells from single-cell RNA sequencing (scRNA-seq) experiments. Validated on both simulated and real data, sciCSR re-analyzes scRNA-seq alignments to differentiate productive heavy-chain immunoglobulin transcripts from germline ‘sterile’ transcripts. From a snapshot of B cell scRNA-seq data, a Markov state model is built to infer the dynamics and direction of CSR. Applying sciCSR on severe acute respiratory syndrome coronavirus 2 vaccination time-course scRNA-seq data, we observe that sciCSR predicts, using data from an earlier time point in the collected time-course, the isotype distribution of B cell receptor repertoires of subsequent time points with high accuracy (cosine similarity ~0.9). Using processes specific to B cells, sciCSR identifies transitions that are often missed by conventional RNA velocity analyses and can reveal insights into the dynamics of B cell CSR during immune response.
Structure of the transcribing RNA polymerase II–Elongin complex
Authors: Chen Ying , Kokic Goran , Dienemann Christian , Dybkov Olexandr , Urlaub Henning , Cramer Patrick 
Published: November 2023

AbstractElongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB–ELOC subunit heterodimer. ELOA contains a ‘latch’ that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element.
9-oxo-ODAs suppresses the proliferation of human cervical cancer cells through the inhibition of CDKs and HPV oncoproteins
Authors: Mogi Kazumasa , Koya Yoshihiro , Yoshihara Masato , Sugiyama Mai , Miki Rika , Miyamoto Emiri , Fujimoto Hiroki , Kitami Kazuhisa , Iyoshi Shohei , Tano Sho , Uno Kaname , Tamauchi Satoshi , Yokoi Akira , Shimizu Yusuke , Ikeda Yoshiki , Yoshikawa Nobuhisa , Niimi Kaoru , Yamakita Yoshihiko , Tomita Hiroyuki , Shibata Kiyosumi , Nawa Akihiro , Tomoda Yutaka , Kajiyama Hiroaki 
Published: November 2023

AbstractMucosal human papillomavirus (HPV) subtypes 16 and 18 are causative agents of cervical cancer, a leading cause of cancer-related deaths among women worldwide. In Japan, eggplant calyx is a folk remedy used to treat common warts. 9-oxo-(10E,12E)-octadecadienoic acid, isolated from eggplant calyx, may have antitumor effects. This study investigated the antitumor effects of 9-oxo-(10E, 12Z)-octadecadienoic acid and 9-oxo-(10E,12E)-octadecadienoic acid (9-oxo-ODAs) on human cervical cancer cells. 9-oxo-ODAs suppressed the proliferation of human cervical cancer cell lines (HeLa, and SiHa) in a concentration-dependent manner (IC50 = 25–50 µM). FCM analysis revealed that 9-oxo-ODAs induced apoptosis. Transcriptome, proteomics, and enrichment analyses revealed that treatment with 9-oxo-ODAs significantly altered the cell cycle and p53 pathways and decreased cyclin-dependent kinase 1 (CDK1) protein expression. Real-time PCR analysis demonstrated that 9-oxo-ODAs reduced CDK1 mRNA expression in a concentration-dependent manner. In vitro, 9-oxo-ODAs reduced the HPV oncoprotein expression. In ex vivo human cervical cancer tissues, 9-oxo-ODAs decreased CDK1 expression and increased cleaved caspase 3, an apoptosis marker. Further, 9-oxo-ODAs showed the potential to suppressed metastatic formation and growth of cervical cancer in vivo. These findings suggest that 9-oxo-ODAs induce cell cycle arrest and apoptosis in HPV-positive human cervical cancer cells, and this process involves CDK1. Consequently, 9-oxo-ODAs may be potential therapeutic agents for cervical cancer.
Evaluation of optimal methods and ancestries for calculating polygenic risk scores in East Asian population
Authors: Kim Dong Jun , Kang Joon Ho , Kim Ji-Woong , Cheon Myeong Jae , Kim Sun bin , Lee Young Kee , Lee Byung-Chul 
Published: November 2023

AbstractPolygenic risk scores (PRSs) have been studied for predicting human diseases, and various methods for PRS calculation have been developed. Most PRS studies to date have focused on European ancestry, and the performance of PRS has not been sufficiently assessed in East Asia. Herein, we evaluated the predictive performance of PRSs for East Asian populations under various conditions. Simulation studies using data from the Korean cohort, Health Examinees (HEXA), demonstrated that SBayesRC and PRS-CS outperformed other PRS methods (lassosum, LDpred-funct, and PRSice) in high fixed heritability (0.3 and 0.7). In addition, we generated PRSs using real-world data from HEXA for ten diseases: asthma, breast cancer, cataract, coronary artery disease, gastric cancer, glaucoma, hyperthyroidism, hypothyroidism, osteoporosis, and type 2 diabetes (T2D). We utilized the five previous PRS methods and genome-wide association study (GWAS) data from two biobank-scale datasets [European (UK Biobank) and East Asian (BioBank Japan) ancestry]. Additionally, we employed PRS-CSx, a PRS method that combines GWAS data from both ancestries, to generate a total of 110 PRS for ten diseases. Similar to the simulation results, SBayesRC showed better predictive performance for disease risk than the other methods. Furthermore, the East Asian GWAS data outperformed those from European ancestry for breast cancer, cataract, gastric cancer, and T2D, but neither of the two GWAS ancestries showed a significant advantage on PRS performance for the remaining six diseases. Based on simulation data and real data studies, it is expected that SBayesRC will offer superior performance for East Asian populations, and PRS generated using GWAS from non-East Asian may also yield good results.
Optical valley separation in two-dimensional semimetals with tilted Dirac cones
Authors: Wild Andrew , Mariani Eros , Portnoi M. E. 
Published: November 2023

AbstractQuasiparticles emerging in crystalline materials can possess a binary flavor known as the valley quantum number which can be used as a basis to encode information in an emerging class of valleytronic devices. Here we show that two-dimensional semimetals with tilted Dirac cones in the electronic band structure exhibit spatial separation of carriers belonging to different valleys under illumination. In stark contrast to gapped Dirac materials this optovalleytronic phenomenon occurs in systems with intact inversion and time-reversal symmetry that host gapless Dirac cones in the band structure, thereby retaining the exceptional graphene-like transport properties. We thus demonstrate that optical valley separation is possible at arbitrarily low photon frequencies including the deep infrared and terahertz regimes with full gate tunability via Pauli blocking. As a specific example of our theory, we predict tunable valley separation in the proposed two-dimensional tilted Dirac cone semimetal 8-Pmmn borophene for incident infrared photons at room temperature. This work highlights the potential of two-dimensional tilted Dirac cone materials as a platform for tunable broadband optovalleytronic applications.
T2 mapping for quantitative assessment of ankle cartilage of weightlifters
Authors: Wu Weibiao , Kang Zhuanzhuan , Mu Di , Zhao Huiyu , Yang Feng 
Published: November 2023

AbstractThe research into the prevention of sports injuries among the population, particularly juveniles, has become crucial due to the increasing participation in physical exercises like fitness. To assess the difference in T2 values of ankle talar cartilage between weightlifters and healthy volunteers using quantitative magnetic resonance imaging (MRI) technique T2 mapping. Study design: Prospective. Prospective evaluation of T2 values of ankle cartilage of 50 weightlifters (30 adults and 20 juveniles) and 100 healthy volunteers (80 adults and 20 juveniles) using Siemens 3.0 T MRI with PDWI, T1WI, and T2 mapping sequences. Three physicians manually divided the talar cartilage of the ankle joint into six regions of interest. Three physicians utilized the anterior and posterior cut edges of the tibial cartilage as markers to identify the corresponding anterior and posterior cut edges of the talar cartilage on the sagittal MRI images. The medial and lateral sides were defined as half of the talar articular surface on the coronal plane. Differences in T2 values in each cartilage region were compared using independent sample T test or Mann–Whitney U test. The T2 values of talar cartilage were significantly increased in the athlete group relative to the volunteer group (35.11 and 31.99, P < 0.001), with the most significant difference observed in the juvenile athlete group compared to the volunteer group (34.42 and 28.73, P < 0.001). There was a significant difference in the T2 value of ankle talar cartilage between weightlifters and healthy volunteers, and juveniles may be more vulnerable to overuse sports injuries. This study contributes to understanding the cartilage health of juvenile athletes and the prevention of sports injuries.
Engineering planar antenna using geometry arrangements for wireless communications and satellite applications
Authors: El-Hakim Hesham A. , Mohamed Hesham A. 
Published: November 2023

AbstractA triple-band microstrip patch antenna designed for the IEEE 802.16e WiMAX, IEEE 802.11a WLAN, C-band downlink communications, and Ku-band radar recent applications is suggested in this article. The planned antenna operates at 2.45, 6, and 14 GHz resonant frequencies. The antenna fulfilled triple-band physical characteristics covering industrial, scientific, and medical (ISM) bands between (2.1–2.8) GHz; (5.6–6.5) GHz for wireless local area network (WLAN) or ultra-wideband (UWB) services; and 12.7–16 GHz for future two-way 5G:6G either broadcasting or mobile satellite communications. To achieve better return loss performance, parametric studies are carried out using Microwave Studio (CST MWS). The proposed antenna is designed on the FR4 as a hosting medium of total size 46 × 38 × 1.6 mm3, combined with a planar transmission line (T.L.) feed and defected ground structure (DGS). The simulated antenna’s input reflection coefficient (S11) results and the far-field measurements show good agreement. The fabricated prototype achieves peak gain values of 2.8, 3.8, and 4.7 dBi, respectively, and bidirectional radiation characteristics. A comparative study with other recent publications is implemented to validate the consistency of the design.
Mercury and CO2 emissions from artisanal gold mining in Brazilian Amazon rainforest
Authors: Fritz Benjamin , Peregovich Bernhard , da Silva Tenório Lorena , da Silva Alves Adria Cristina , Schmidt Mario 
Published: November 2023

AbstractThe Tapajós River basin in Brazil is one of the world’s regions most affected by artisanal gold mining (ASGM), which is responsible for the release of mercury and high energy consumption. Mercury, mixed with gold-containing materials and then released through heating to extract the gold, can be recovered using a simple distillation device called a retort. Use of these tools has now become standard. In a comprehensive study, we investigated the use of mercury and energy at 47 mining sites in the Tapajós River basin. These included numerous mines that were operated informally or in some cases even illegally and are therefore not accessible to outsiders. Our survey shows that 1.7 kg of mercury are used per kg of gold extracted, of which only about 0.19 kg of mercury is released into the environment when retorts are used. Overall, this means an annual release of at least ≈2.5 tonnes of mercury in the region, even when retorts are used. We also find that ASGM contributes to climate change through energy consumption responsible for the release of about 16,000 kg of CO2 equivalent per kilogram of gold. This means that even artisanal gold mining, which uses retorts, has a major environmental impact.