bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apoplastic pH determines the hypocotyl response to auxin dosage and light
Authors: Wei Ning , Wang Jiajun , Jin Dan , Deng Zhaoguo , Song Zihao , Zheng Lidan , Zeng Haiyue , Kinoshita Toshinori , Liao Zhihua , Chen Haodong , Deng Xingwang 
Published: December 2023

Abstract

The phytohormone auxin and light both regulate plant elongation growth. Light suppresses hypocotyl elongation, whereas auxin promotes it. However, auxin can reverse its effect and inhibit elongation when applied to etiolated seedlings or in high dosages. How dosages or light conditions change the effect of auxin on hypocotyl growth has long been mysterious. We found that, regardless of the dosage, more auxin induces more transcription of SAURs (Small Auxin-Up RNAs), leading to a stronger activation of plasma membrane proton pump H+-ATPases (AHAs), and consequently, progressive acidification of the apoplast in hypocotyls. Apoplastic acidification promotes growth, but when the pH drops below a threshold, further acidification inhibits elongation. The short hypocotyl phenotype caused by auxin overdosage can be alleviated by inactivating the AHA activity. Light irradiation downregulates SAUR levels and decreases AHA activity in the hypocotyl. Light-grown hypocotyls exhibit a higher apoplastic pH, which impedes cell elongation and counteracts auxin induced over-acidification. Our findings indicate that the biphasic effect of auxin results from the biphasic response of cell elongation to decreasing apoplastic pH. Auxin and light antagonistically regulate the SAUR-PP2C.D-AHA pathway, eventually achieving the apoplastic pH appropriate for the hypocotyl growth of the given environment.
The peculiar precursor of a gamma-ray burst from a binary merger involving a magnetar
Authors: Xiong Shaolin , Xiao Shuo , Zhang Yan-Qiu , Zhu Zi-Pei , Gao He , Xu Dong , Zhang Shuang-Nan , Peng Wenxi , Li X.B. , Zhang Peng , Lu Fangjun , Lin Lin , Liu Liang-Duan , Zhang Zhen , Ge Mingyu , Tuo Y.L. , Xue Wang-Chen , Fu Shao-Yu , Liu Xing , Liu Jin-Zhong , Li An , Wang Tian-Cong , Zheng Chao , Wang Yue , Jiang Shuai-Qing , Li Jin-Da , Liu Jia-Cong , Cao Zhou-Jian , Luo Xi-Hong , Yang Jiao-Jiao , Yi Shu-Xu , Wang Xi-Lu , Cai C. , Yi Q.B. , Zhao Yi , Xie Sheng-Lun , Li C.K. , Luo Qi , Liao Jin-Yuan , Song Liming , Zhang Shu , Qu J.L. , Liu C.Z. , Li Xu-Fang , Xu Y.P. , Li Tipei 
Published: December 2023

Abstract
The milestone discovery of GW 170817-GRB 170817A-AT 2017gfo1 has shown that gravitational wave (GW) could be produced during the merger of neutron star-neutron star/black hole and that in electromagnetic (EM) wave a gamma-ray burst (GRB) and a kilonova (KN) are generated in sequence after the merger. Observationally, however, EM property before the merger phase is still unclear. Here we report a peculiar precursor in a KN-associated long-duration GRB 211211A, providing evidence of the EM before the merger. This precursor lasts ∼ 0.2 s, and the waiting time between the precursor and the main burst is ∼ 1 s, comparable to that between GW 170817 and GRB 170817A. The spectrum of the precursor could be well fit with a non-thermal cutoff power-law (CPL) model instead of a blackbody. Especially, an Quasi-Periodic Oscillation (QPO) with frequency of ∼22 Hz is most likely detected in the precursor. These temporal and spectral properties indicate that this precursor is probably produced by a catastrophic flare accompanying with magnetoelastic or crustal oscillations of a magnetar in binary compact merger2. The strong magnetic field of the magnetar can also account for the prolonged duration of GRB 211211A. However, it poses a challenge to reconcile the rather short lifetime of a magnetar3 with the rather long spiraling time of a binary neutron star system only by the GW radiation before merger.
The potential of hydrolates for use in the production of alfalfa micro sprouts: sanitizers and flavour enhancers
Authors: Acimovic Milica , Samardžić Nataša , Šovljanski Olja , Lončar Biljana , Jeremić Jovana Stanković , Pezo Lato , Konstantinović Bojan , Vasiljević Sanja 
Published: December 2023

Abstract

Sprouted seeds and microgreens are emerging as innovative specialty raw salad crops, valued for their health-promoting properties. However, the risk of foodborne illnesses associated with microbial contamination in microgreens underscores the need for effective sanitization in their production. This study explores using hydrolates, by-products of essential oil distillation from six plants, as natural sanitizers in alfalfa microgreen production. The research investigates their impact on seed germination, antimicrobial activity, and sensory attributes. Results revealed that oregano, fennel, lavender, and lemon catmint hydrolates decrease alfalfa seed germination, while peppermint and hop hydrolates have no significant impact. Peppermint and fennel hydrolates demonstrate notable efficacy in antimicrobial testing. Sensory analysis indicates differences in odour and flavour, with peppermint, oregano, and lavender receiving high scores. According to the results, peppermint hydrolate can be considered a favourable option for alfalfa micro sprout production, contributing to sustainable and organic approaches in urban agriculture and underlining the importance of natural sanitizers for food safety.
Assembly and comparative analysis of the complete mitochondrial genome of Saussurea inversa (Asteraceae)
Authors: Dai Wubin , Ju Xiuting , Shi Guomin , He Tao 
Published: December 2023

Abstract
Saussurea inversa is a perennial herb used in traditional Chinese medicine and is effective against rheumatoid arthritis. In this study, we sequenced the complete mitochondrial(mt) genome of S. inversa (GenBank accession number: ON584565.1). The circular mt genome of S. inversa was 335,372 bp in length, containing 62 genes, including 33 mRNAs, 22 tRNAs, six rRNAs, and one pseudo-gene, with 1,626 open reading frames. The GC content was 45.14%. Predictive analysis of substantial RNA-editing of its presence found that the most abundant RNA editing is ccmFn, with 36. Gene migration was observed to occur between the mt and chloroplast(cp) genomes of S. inversa via the detection of homologous gene fragments. Phylogenetic analysis revealed that S. inversa was clustered with Arctium tomentosum (Asteraceae). Our findings provide extensive information regarding the mt genome of S. inversa and help lay the foundation for future studies on the genetic variations, phylogeny, and breeding of S. inversa via an analysis of the mt genome.
Fibroblast activation protein regulates natural killer cell migration, extravasation and tumor infiltration
Authors: Weiner Louis , Fitzgerald Allison , Maynard Rachael , Marcisak Emily , Nasir Apsra , Glasgow Eric , Jablonski Sandra , Veken Pieter Van Der , Pearson Gray , Eisman Shira , Mace Emily , Fertig Elana 
Published: December 2023

Abstract
Natural killer (NK) cells play a critical role in physiologic and pathologic conditions such as pregnancy, infection, autoimmune disease and cancer. In cancer, numerous strategies have been designed to exploit the cytolytic properties of NK cells, with variable success. A major hurdle to NK-cell focused therapies is NK cell recruitment and infiltration into tumors. While the chemotaxis pathways regulating NK recruitment to different tissues are well delineated, the mechanisms human NK cells employ to physically migrate are ill-defined. We show for the first time that human NK cells express fibroblast activation protein (FAP), a cell surface protease previously thought to be primarily expressed by activated fibroblasts. FAP degrades the extracellular matrix to facilitate cell migration and tissue remodeling. We used novel in vivo zebrafish and in vitro 3D culture models to demonstrate that FAP knock out and pharmacologic inhibition restrict NK cell migration, extravasation, and invasion through tissue matrix. Notably, forced overexpression of FAP promotes NK cell invasion through matrix in both transwell and tumor spheroid assays, ultimately increasing tumor cell lysis. Additionally, FAP overexpression enhances NK cells invasion into a human tumor in immunodeficient mice. These findings demonstrate the necessity of FAP in NK cell migration and present a new approach to modulate NK cell trafficking and enhance cell-based therapy in solid tumors.
An archaeal chromatin protein condenses DNA through bridging-induced phase separation
Authors: Zhang Zhenfeng , Ding Niannian , Wang Mengxue , Li Haodun , Sun Fei , Chen Yuanyuan , Yang Yunfeng , Zhang Yi , Huang Junkai , Dai Xin , Shen Yulong , Fu Yu , Huang Li 
Published: December 2023

Abstract
Phase separation serves an important role in the three-dimensional chromosome organization and remodeling in eukaryotes. Whether this process is involved in archaeal chromosome organization is unknown. Here we demonstrate that archaeal DNA condensing protein1 (aDCP1) from the hyperthermophilic crenarchaeon Sulfolobus islandicus is able to bridge DNA efficiently and form large protein-DNA condensates with a droplet- or gel-like morphology in vitro. Within the condensates, aDCP1 exhibits a fast dynamic while the DNA appears in a solid-like state. At the single-molecule level, aDCP1 efficiently compacts DNA through a three-step mechanism, which presumably entails the clustering of aDCP1 on the DNA and the subsequent fusion of the clusters. Deletion of the aDCP1 gene results in noticeable changes in chromosome conformation in S. islandicus, which are characterized by enhanced interactions between the A and B compartments and reduced interactions within the self-interacting domains as well as between domains in the same compartment. Taken together, our results indicate that aDCP1 is capable of inducing DNA bridging-induced phase separation and serves a role in chromosome organization in the organism.
Sex differences in mitochondrial gene expression during viral myocarditis
Authors: Florio Damian Di , Gorelov David , McCabe Elizabeth , Beetler Danielle , Shapiro Katie , Bruno Katelyn , Chekuri Isha , Jain Angita , Whelan Emily , Salomon Gary , Khatib Sami , Bonvie-Hill Natalie , Giresi Presley , Balamurugan Varsini , Weigel Gabriel , Fliess Jessica , Darakjian Ashley , Edenfield Brandy , Kocsis Christian , McLeod Christopher , Cooper Leslie , Audet-Walsh Etienne , Coronado Michael , Sin Jon , Fairweather DeLisa 
Published: December 2023

Abstract

Background
Myocarditis is an inflammation of the heart muscle most often caused by an immune response to viral infections. Sex differences in the immune response during myocarditis have been well described but upstream mechanisms in the heart that might influence sex differences in disease are not completely understood.
Methods
Male and female BALB/c wild type mice received an intraperitoneal injection of heart-passaged coxsackievirus B3 (CVB3) or vehicle control. Bulk-tissue RNA-sequencing was conducted to better understand sex differences in CVB3 myocarditis. We performed enrichment analysis to understand sex differences in the transcriptional landscape of myocarditis and identify candidate transcription factors that might drive sex differences in myocarditis.
Results
The hearts of male and female mice with myocarditis were significantly enriched for pathways related to an innate and adaptive immune response compared to uninfected controls. When comparing females to males with myocarditis, males were enriched for inflammatory pathways and gene changes that suggested worse mitochondrial transcriptional support (e.g., mitochondrial electron transport genes). In contrast, females were enriched for pathways related to mitochondrial respiration and bioenergetics, which were confirmed by higher transcript levels of master regulators of mitochondrial function including peroxisome proliferator-activated receptor gamma coactivator 1 (PGC1α), nuclear respiratory factor 1 (NRF1) and estrogen-related receptor alpha (ERRα). TRANSFAC analysis identified ERRa as a transcription factor that may mediate sex differences in mitochondrial function during myocarditis.
Conclusions
Master regulators of mitochondrial function were elevated in females with myocarditis compared to males and may promote sex differences in mitochondrial respiratory transcript expression during viral myocarditis resulting in less severe myocarditis in females following viral infection.
Increase of prostate specific antigen doubling time predicts survival in metastatic castration-resistant prostate cancer patients undergoing [223Ra]RaCl2 therapy
Authors: Lu Hsi-Huei , Chiu Nan-Tsing , Tsai Mu-Hung 
Published: December 2023

Abstract
Background
[223Ra]RaCl2 is an important treatment modality for bone-dominant metastatic castration-resistant prostate cancer (mCRPC). However, there is currently a lack of effective markers to monitor treatment response during the course of treatment. We retrospectively collected data from mCRPC patients who underwent [223Ra]RaCl2 treatment at our institution between August 2020 and June 2023. Prostate specific antigen (PSA) measurements prior to treatment and during treatment were collected. Baseline PSADT was calculated from PSA measurements prior to [223Ra]RaCl2 treatment; interim PSADT was calculated from PSA measurements before [223Ra]RaCl2 treatment and prior to the 4th course injection. Overall survival was calculated from start of treatment to the date of death. Univariable and multivariable analysis using the Cox proportional hazards model were performed to examine the association of factors with overall survival.
Results
We included 35 patients from our institution, with a median overall survival of 13.3 months. Eighteen (51.4%) completed all six courses of treatment. PSADT response (interim PSADT > baseline PSADT or decreased PSA) was observed in 20 patients. Overall survival was associated with a PSADT response (HR = 0.318, 95% CI 0.133–0.762, p = 0.010) when compared to patients without a PSADT response.
Conclusions
Dynamic changes in PSADT were associated with survival in mCRPC patients receiving [223Ra]RaCl2 therapy. Comparing interim and baseline PSADT could serve as a valuable marker for determining treatment benefit.
Tracing the Invisible Mutant ADNP protein in Helsmoortel- Van der Aa Syndrome patients
Authors: D'Incal Claudio Peter , Cappuyns Elisa , Choukri Kaoutar , De Man Kevin , Szrama Kristy , Konings Anthony , Bastini Lina , Gabriele Michele , Rizzuti Ludovico , Vitriolo Alessandro , Testa Giuseppe , Mohn Fabio , Bühler Marc , Aa Nathalie Van der , Dijck Anke Van , Kooy R. Frank , Berghe Wim Vanden 
Published: December 2023

Abstract
Heterozygous de novo mutations in the Activity-Dependent Neuroprotective Homeobox (ADNP) gene underlie Helsmoortel-Van der Aa syndrome (HVDAS). Most of these mutations are situated in the last exon and we previously demonstrated escape from nonsense-mediated decay by detecting mutant ADNP mRNA in patient blood. In this study, wild-type and ADNP mutants are investigated at the protein level and therefore optimal detection of the protein is required. Detection of ADNP by means of western blotting has been ambiguous with reported antibodies resulting in non-specific bands without unique ADNP signal. Validation of an N-terminal ADNP antibody (Aviva Systems) using a blocking peptide competition assay allowed to differentiate between specific and non-specific signals in different sample materials, resulting in a unique band signal around 150 kDa for ADNP, above its theoretical molecular weight of 124 kDa. Detection with different C-terminal antibodies confirmed the signals at an observed molecular weight of 150 kDa. Our antibody panel was subsequently tested by immunoblotting comparing parental and homozygous CRISPR/Cas9 endonuclease-mediated Adnp knockout cell lines, showing disappearance of the 150 kDa signal, indicative for intact ADNP. By means of both a GFPSpark and Flag-tag N-terminally fused to a human ADNP expression vector, we detected wild-type ADNP together with mutant forms after introduction of patient mutations in E. coli expression systems by site-directed mutagenesis. Furthermore, we were also able to visualize endogenous ADNP with our C-terminal antibody panel in heterozygous cell lines carrying ADNP patient mutations, while the truncated ADNP mutants could only be detected with epitope-tag-specific antibodies, suggesting that addition of an epitope-tag possibly helps stabilizing the protein. However, western blotting of patient-derived hiPSCs, immortalized lymphoblastoid cell lines and post-mortem patient brain material failed to detectnative mutant ADNP protein,whereas alternative experimental protein enrichment strategies such as co-immunoprecipitation and mass spectrometry also depend on appropriately characterized antibodies that are not currently available. This study aims to shape awareness for critical assessment of ADNP mutant protein analysis in Helsmoortel-Van der Aa syndrome.
VEXAS Syndrome: Complete molecular remission after hypomethylating therapy
Authors: Sockel Katja , Goetze Katharina , Ganster Christina , Bill Marius , Georgi Julia-Annabell , Balaian Ekaterina , Aringer Martin , Trautmann Karolin , Uhlig Maria , Bornhäuser Martin , Haase Detlef , Thiede Christian 
Published: December 2023

Abstract
The Vexas syndrome, a genetically defined autoimmune disease, associated with various hematological neoplasms has been attracting growing attention since its initial description in 2020. While various therapeutic strategies have been explored in case studies, the optimal treatment strategy is still under investigation and allogeneic cell transplantation is considered the only curative treatment. Here, we describe 2 patients who achieved complete molecular remission of the underlying UBA1 mutant clone outside the context of allogeneic HCT. Both patients received treatment with the hypomethylating agent Azacitidine, and deep molecular remission triggered treatment de-escalation and even cessation with sustained molecular remission in one of them. Prospective studies are necessary to clarify which VEXAS patients will benefit most from hypomethylating therapy and to understand the variability in the response to different treatment strategies.
The effect of lining hydraulic properties on the efficiency and cost of irrigation canal reconstruction
Authors: Zelenakova Martina , Zeleňáková Martina , Arifjanov Aybek , Abd-Elhamid Hany F. , Gergeľová Marcela Bindzárová , Fatxulloyev Alisher , Allayorov Davronjon 
Published: December 2023

Abstract
Irrigation canals play an important role in the economic development of Uzbekistan which is located in arid zone and shared user of transboundary water resources. Almost three fourth of the irrigation network in Uzbekistan is unlined that subject to some natural processes such as vegetation, erosion, sedimentation, and seepage. The efficiency of the irrigation networks in Uzbekistan is about 63%. Lining of canals is the major protection measure against water scarcity for Uzbekistan. This study aims to investigate how the hydraulic properties of different lining materials such as geomembrane, concrete, asphalt, sand mixed bentonite and stone pitching affect the rehabilitation cost of canals. In this study, field data and hydrodynamic model HEC-RAC are used for analysis of using different lining materials on the efficiency of the canal and then the costs of rehabilitation were compared. To apply the hydrodynamic model HEC-RAS, flow and bathymetric parameters were measured by employing the acoustic Doppler current profiler system for a reach of length 1.0 km in Tashkent magistral canal. The obtained R2 between modeled and measured data equals to 0.86. The use of different lining materials such as geomembrane, concrete, asphalt, sand mixed bentonite and stone pitching affect the channel geometry with different ranges from 21.69 to 34.41 per running meter (RMT). With different cross-sectional values, rehabilitation of the first reach of Toshkent magistral canal costs about $ 260, 688, 536, 286, 210 thousand respectively. In the point of lifetime, geomembrane then concrete, and stone pitching showed the minimum annual coverage value containing $32, 46, 10 thousand per year respectively. Stone pitching with the longest durability is the most efficient technique to improve water-use efficiency of Toshkent magistral canal. This study could help the policy makers to select the best material for lining based on the lifetime, cost and durability.
Selection of Track Form in Railway Tunnel from a Life Cycle Analysis Perspective
Authors: Prokopov Andrej , Aava Birgitta Olsson , Famurewa Stephen Mayowa , Rantatalo Matti 
Published: December 2023

Abstract

The use of greenhouse gas emissions as a criterion for decision-making within the rail industry is increasing. The demand for the consideration of this criterion affects the type of decision models acceptable by railway infrastructure managers in the planning, construction, and maintenance of railway assets. The total amount of greenhouse gas emitted from a track solution in tunnels during its service life depends on the track form (i.e., ballasted track or the ballastless track), the type of construction, maintenance machines used, the current traffic profile, and the length of the tunnel. However, the development in the design of ballastless track systems during recent decades to make them environmentally friendly is a motivation for infrastructure managers to rethink and consider the use of the system. This paper addresses the effect of applying the optimized ballastless track system Rheda 2000® in a railway tunnel (the Hallsberg-Stenkumla tunnel) as part of a new line project in Sweden. The greenhouse gas emissions, represented by life cycle CO2 equivalent emission is calculated using the climate impact software developed by the Swedish Transport Administration Trafikverket. The result is compared with the estimated emission from the conventional ballasted tracks. The study shows that CO2 equivalent emissions by a ballastless track during its life cycle is 10% lower than that of the ballasted track. The primary total emission driver for both track form solutions is the emissions generated at the manufacturing of rails. The second important emission factor for the ballasted track solution is the emission from the renewal of the track form during its life cycle. The second important emission factor for the ballastless track solution is concrete manufacturing. The model applied in the study is an integral part of an integrated decision support system for effectively selecting track solutions from a lifecycle perspective.