bluuebunny/crossref_metadata_2025_split huggingface dataset:
Promoter editing for the genetic improvement of crops
Authors: Shi Lu , Su Jing , Cho Myeong-Je , Song Hao , Dong Xiaoou , Liang Ying , Zhang Zhiyong 
Published: May 2023

Abstract
Gene expression plays a fundamental role in the regulation of agronomically important traits in crop plants. The genetic manipulation of plant promoters through genome editing has emerged as an effective strategy to create favorable traits in crops by altering the expression pattern of the pertinent genes. Promoter editing can be applied in a directed manner, where nucleotide sequences associated with favorable traits are precisely generated. Alternatively, promoter editing can also be exploited as a random mutagenic approach to generate novel genetic variations within a designated promoter, from which elite alleles are selected based on their phenotypic effects. Pioneering studies have demonstrated the potential of promoter editing in engineering agronomically important traits as well as in mining novel promoter alleles valuable for plant breeding. In this review, we provide an update on the application of promoter editing in crops for increased yield, enhanced tolerance to biotic and abiotic stresses, and improved quality. We also discuss several remaining technical bottlenecks and how this strategy may be better employed for the genetic improvement of crops in the future.
Phytochrome-interacting factor PIF3 integrates phytochrome B and UV-B signaling pathways to regulate gibberellin- and auxin-dependent growth in cucumber hypocotyls
Authors: Zhao Jianyu , Bo Kailiang , Pan Yupeng , Li Yuhong , Yu Daoliang , Li Chuang , Chang Jiang , Wu Shuang , Wang Zhongyi , Zhang Xiaolan , Gu Xingfang , Weng Yiqun 
Published: May 2023

Abstract
In Arabidopsis, the photoreceptors phytochrome B (PhyB) and UV-B resistance 8 (UVR8) mediate light responses that play a major role in regulating photomorphogenic hypocotyl growth, but how they crosstalk to coordinate this process is not well understood. Here we report map-based cloning and functional characterization of an ultraviolet (UV)-B-insensitive, long-hypocotyl mutant, lh1, and a wild-type-like mutant, lh2, in cucumber (Cucumis sativus), which show defective CsPhyB and GA oxidase2 (CsGA20ox-2), a key gibberellic acid (GA) biosynthesis enzyme, respectively. The lh2 mutation was epistatic to lh1 and partly suppressed the long-hypocotyl phenotype in the lh1lh2 double mutant. We identified phytochrome interacting factor (PIF) CsPIF3 as playing a critical role in integrating the red/far-red and UV-B light responses for hypocotyl growth. We show that two modules, CsPhyB–CsPIF3–CsGA20ox-2–DELLA and CsPIF3–auxin response factor 18 (CsARF18), mediate CsPhyB-regulated hypocotyl elongation through GA and auxin pathways, respectively, in which CsPIF3 binds to the G/E-box motifs in the promoters of CsGA20ox-2 and CsARF18 to regulate their expression. We also identified a new physical interaction between CsPIF3 and CsUVR8 mediating CsPhyB-dependent, UV-B-induced hypocotyl growth inhibition. Our work suggests that hypocotyl growth in cucumber involves a complex interplay of multiple photoreceptor- and phytohormone-mediated signaling pathways that show both conservation with and divergence from those in Arabidopsis.
Spatiotemporal patterns of wheat response toPyrenophora tritici-repentisin asymptomatic regions revealed by transcriptomic and X-ray fluorescence microscopy analyses
Authors: Moolhuijzen Paula , Sanglard Lilian M V P , Paterson David J , Gray Sean , Khambatta Karina , Hackett Mark J , Zerihun Ayalsew , Gibberd Mark R , Naim Fatima 
Published: May 2023

AbstractPathogen attacks elicit dynamic and widespread molecular responses in plants. While our understanding of plant responses has advanced considerably, little is known of the molecular responses in the asymptomatic ‘green’ regions adjoining lesions. Here, we explore gene expression data and high-resolution elemental imaging to report the spatiotemporal changes in the asymptomatic green region of susceptible and moderately resistant wheat cultivars infected with a necrotrophic fungal pathogen, Pyrenophora tritici-repentis. We show, with improved spatiotemporal resolution, that calcium oscillations are modified in the susceptible cultivar, resulting in ‘frozen’ host defence signals at the mature disease stage, and silencing of the host’s recognition and defence mechanisms that would otherwise protect it from further attacks. In contrast, calcium accumulation and a heightened defence response were observed in the moderately resistant cultivar in the later stage of disease development. Furthermore, in the susceptible interaction, the asymptomatic green region was unable to recover after disease disruption. Our targeted sampling technique also enabled detection of eight previously predicted proteinaceous effectors in addition to the known ToxA effector. Collectively, our results highlight the benefits of spatially resolved molecular analysis and nutrient mapping to provide high-resolution spatiotemporal snapshots of host–pathogen interactions, paving the way for disentangling complex disease interactions in plants.
A 1.55 R⊕ habitable-zone planet hosted by TOI-715, an M4 star near the ecliptic South Pole
Authors: Dransfield Georgina , Timmermans Mathilde , Triaud Amaury H M J , Dévora-Pajares Martín , Aganze Christian , Barkaoui Khalid , Burgasser Adam J , Collins Karen A , Cointepas Marion , Ducrot Elsa , Günther Maximilian N , Howell Steve B , Murray Catriona A , Niraula Prajwal , Rackham Benjamin V , Sebastian Daniel , Stassun Keivan G , Zúñiga-Fernández Sebastián , Almenara José Manuel , Bonfils Xavier , Bouchy François , Burke Christopher J , Charbonneau David , Christiansen Jessie L , Delrez Laetitia , Gan Tianjun , García Lionel J , Gillon Michaël , Gómez Maqueo Chew Yilen , Hesse Katharine M , Hooton Matthew J , Isopi Giovanni , Jehin Emmanuël , Jenkins Jon M , Latham David W , Mallia Franco , Murgas Felipe , Pedersen Peter P , Pozuelos Francisco J , Queloz Didier , Rodriguez David R , Schanche Nicole , Seager Sara , Srdoc Gregor , Stockdale Chris , Twicken Joseph D , Vanderspek Roland , Wells Robert , Winn Joshua N , de Wit Julien , Zapparata Aldo 
Published: May 2023

ABSTRACT
A new generation of observatories is enabling detailed study of exoplanetary atmospheres and the diversity of alien climates, allowing us to seek evidence for extraterrestrial biological and geological processes. Now is therefore the time to identify the most unique planets to be characterized with these instruments. In this context, we report on the discovery and validation of TOI-715 b, a $R_{\rm b}=1.55\pm 0.06\rm R_{\oplus }$ planet orbiting its nearby (42 pc) M4 host (TOI-715/TIC 271971130) with a period $P_{\rm b} = 19.288004_{-0.000024}^{+0.000027}$ d. TOI-715 b was first identified by TESS and validated using ground-based photometry, high-resolution imaging and statistical validation. The planet’s orbital period combined with the stellar effective temperature $T_{\rm eff}=3075\pm 75~\rm K$ give this planet an installation $S_{\rm b} = 0.67_{-0.20}^{+0.15}~\rm S_\oplus$, placing it within the most conservative definitions of the habitable zone for rocky planets. TOI-715 b’s radius falls exactly between two measured locations of the M-dwarf radius valley; characterizing its mass and composition will help understand the true nature of the radius valley for low-mass stars. We demonstrate TOI-715 b is amenable for characterization using precise radial velocities and transmission spectroscopy. Additionally, we reveal a second candidate planet in the system, TIC 271971130.02, with a potential orbital period of $P_{02} = 25.60712_{-0.00036}^{+0.00031}$ d and a radius of $R_{02} = 1.066\pm 0.092\, \rm R_{\oplus }$, just inside the outer boundary of the habitable zone, and near a 4:3 orbital period commensurability. Should this second planet be confirmed, it would represent the smallest habitable zone planet discovered by TESS to date.
A morphological analysis of the substructures in radio relics
Authors: Wittor D , Brüggen M , Grete P , Rajpurohit K 
Published: May 2023

ABSTRACT
Recent observations of radio relics – diffuse radio emission in galaxy clusters – have revealed that these sources are not smooth but consist of structures in the form of threads and filaments. We investigate the origin of these filamentary structures and the role of projection effects. To this end, we have developed a tool that extracts the filamentary structures from background emission. Moreover, it is capable of studying both two-dimensional and three-dimensional objects. We apply our structure extractor to both observations and cosmological simulations of radio relics. Using Minkowski functionals, we determine the shape of the identified structures. In our 2D analysis, we find that the brightest structures in the observed and simulated maps are filaments. Our analysis of the 3D simulation data shows that radio relics do not consist of sheets but only of filaments and ribbons. Furthermore, we did not find any measurable projection effect that could hide any sheet-like structures in projection. We find that both the magnetic field and the shock front consist of filaments and ribbons that cause filamentary radio emission.
New constraints on cosmological modified gravity theories from anisotropic three-point correlation functions of BOSS DR12 galaxies
Authors: Sugiyama Naonori S , Yamauchi Daisuke , Kobayashi Tsutomu , Fujita Tomohiro , Arai Shun , Hirano Shin’ichi , Saito Shun , Beutler Florian , Seo Hee-Jong 
Published: May 2023

ABSTRACT
We report a new test of modified gravity theories using the large-scale structure of the Universe. This paper is the first attempt to (1) apply a joint analysis of the anisotropic components of galaxy two- and three-point correlation functions (2 and 3PCFs) to actual galaxy data and (2) constrain the non-linear effects of degenerate higher-order scalar-tensor (DHOST) theories on cosmological scales. Applying this analysis to the Baryon Oscillation Spectroscopic Survey (BOSS) data release 12, we obtain the lower bounds of −1.655 &lt; ξt and −0.504 &lt; ξs at the $95{{\ \rm per\ cent}}$ confidence level on the parameters characterizing the time evolution of the tidal and shift terms of the second-order velocity field. These constraints are consistent with GR predictions of ξt = 15/1144 and ξs = 0. Moreover, they represent a 35-fold and 20-fold improvement, respectively, over the joint analysis with only the isotropic 3PCF. We ensure the validity of our results by investigating various quantities, including theoretical models of the 3PCF, window function corrections, cumulative S/N, Fisher matrices, and statistical scattering effects of mock simulation data. We also find statistically significant discrepancies between the BOSS data and the Patchy mocks for the 3PCF measurement. Finally, we package all of our 3PCF analysis codes under the name hitomi and make them publicly available so that readers can reproduce all the results of this paper and easily apply them to ongoing future galaxy surveys.
Pest Alert Tool—a web-based application for flagging species of concern in metabarcoding datasets
Authors: Zaiko Anastasija , Scheel Maximilian , Schattschneider Jessica , von Ammon Ulla , Scriver Michelle , Pochon Xavier , Pearman John K 
Published: May 2023

Abstract
Advances in high-throughput sequencing (HTS) technologies and their increasing affordability have fueled environmental DNA (eDNA) metabarcoding data generation from freshwater, marine and terrestrial ecosystems. Research institutions worldwide progressively employ HTS for biodiversity assessments, new species discovery and ecological trend monitoring. Moreover, even non-scientists can now collect an eDNA sample, send it to a specialized laboratory for analysis and receive in-depth biodiversity record from a sampling site. This offers unprecedented opportunities for biodiversity assessments across wide temporal and spatial scales. The large volume of data produced by metabarcoding also enables incidental detection of species of concern, including non-indigenous and pathogenic organisms. We introduce an online app—Pest Alert Tool—for screening nuclear small subunit 18S ribosomal RNA and mitochondrial cytochrome oxidase subunit I datasets for marine non-indigenous species as well as unwanted and notifiable marine organisms in New Zealand. The output can be filtered by minimum length of the query sequence and identity match. For putative matches, a phylogenetic tree can be generated through the National Center for Biotechnology Information’s BLAST Tree View tool, allowing for additional verification of the species of concern detection. The Pest Alert Tool is publicly available at https://pest-alert-tool-prod.azurewebsites.net/.
GS-SMD server for steered molecular dynamics of peptide substrates in the active site of the γ-secretase complex
Authors: Orzeł Urszula , Pasznik Paweł , Miszta Przemysław , Lorkowski Marcin , Niewieczerzał Szymon , Jakowiecki Jakub , Filipek Sławomir 
Published: May 2023

Abstract
Despite recent advances in research, the mechanism of Alzheimer's disease is not fully understood yet. Understanding the process of cleavage and then trimming of peptide substrates, can help selectively block γ-secretase (GS) to stop overproduction of the amyloidogenic products. Our GS-SMD server (https://gs-smd.biomodellab.eu/) allows cleaving and unfolding of all currently known GS substrates (more than 170 peptide substrates). The substrate structure is obtained by threading of the substrate sequence into the known structure of GS complex. The simulations are performed in an implicit water-membrane environment so they are performed rather quickly, 2–6 h per job, depending on the mode of calculations (part of GS complex or the whole structure). It is also possible to introduce mutations to the substrate and GS and pull any part of the substrate in any direction using the steered molecular dynamics (SMD) simulations with constant velocity. The obtained trajectories are visualized and analyzed in the interactive way. One can also compare multiple simulations using the interaction frequency analysis. GS-SMD server can be useful for revealing mechanisms of substrate unfolding and role of mutations in this process.
Selection of allosteric dnazymes that can sense phenylalanine by expression-SELEX
Authors: Chen Binfen , Yu Xinmei , Gao Ting , Wu Yaoyao , Zhang Xiaojun , Li Sanshu 
Published: May 2023

Abstract
Aptamers are ligand-binding RNA or DNA molecules and have been widely examined as biosensors, diagnostic tools, and therapeutic agents. The application of aptamers as biosensors commonly requires an expression platform to produce a signal to report the aptamer-ligand binding event. Traditionally, aptamer selection and expression platform integration are two independent steps and the aptamer selection requires the immobilization of either the aptamer or the ligand. These drawbacks can be easily overcome through the selection of allosteric DNAzymes (aptazymes). Herein, we used the technique of Expression-SELEX developed in our laboratory to select for aptazymes that can be specifically activated by low concentrations of l-phenylalanine. We chose a previous DNA-cleaving DNAzyme known as II-R1 as the expression platform for its low cleavage rate and used stringent selection conditions to drive the selection of high-performance aptazyme candidates. Three aptazymes were chosen for detailed characterization and these DNAzymes were found to exhibit a dissociation constant for l-phenylalanine as low as 4.8 μM, a catalytic rate constant improvement as high as 20 000-fold in the presence of l-phenylalanine, and the ability to discriminate against closely related l-phenylalanine analogs including d-phenylalanine. This work has established the Expression-SELEX as an effective SELEX method to enrich high-quality ligand-responsive aptazymes.
Dynamic accumulation of cyclobutane pyrimidine dimers and its response to changes in DNA conformation
Authors: Moirangthem Ravina , Gamage Manusha N , Rokita Steven E 
Published: May 2023

Abstract
Photochemical dimerization of adjacent pyrimidines is fundamental to the creation of mutagenic hotspots caused by ultraviolet light. Distribution of the resulting lesions (cyclobutane pyrimidine dimers, CPDs) is already known to be highly variable in cells, and in vitro models have implicated DNA conformation as a major basis for this observation. Past efforts have primarily focused on mechanisms that influence CPD formation and have rarely considered contributions of CPD reversion. However, reversion is competitive under the standard conditions of 254 nm irradiation as illustrated in this report based on the dynamic response of CPDs to changes in DNA conformation. A periodic profile of CPDs was recreated in DNA held in a bent conformation by λ repressor. After linearization of this DNA, the CPD profile relaxed to its characteristic uniform distribution over a similar time of irradiation to that required to generate the initial profile. Similarly, when a T tract was released from a bent conformation, its CPD profile converted under further irradiation to that consistent with a linear T tract. This interconversion of CPDs indicates that both its formation and reversion exert control on CPD populations long before photo-steady-state conditions are achieved and suggests that the dominant sites of CPDs will evolve as DNA conformation changes in response to natural cellular processes.
Atherosclerotic renovascular disease: a clinical practice document by the European Renal Best Practice (ERBP) board of the European Renal Association (ERA) and the Working Group Hypertension and the Kidney of the European Society of Hypertension (ESH)
Authors: Sarafidis Pantelis A , Theodorakopoulou Marieta , Ortiz Alberto , Fernandez-Fernández Beatriz , Nistor Ionut , Schmieder Roland , Arici Mustafa , Saratzis Athanasios , Van der Niepen Patricia , Halimi Jean-Michel , Kreutz Reinhold , Januszewicz Andrzej , Persu Alexandre , Cozzolino Mario 
Published: May 2023

ABSTRACT
Atherosclerotic renovascular disease (ARVD) is the most common type of renal artery stenosis. It represents a common health problem with clinical presentations relevant to many medical specialties and carries a high risk for future cardiovascular and renal events, as well as overall mortality. The available evidence regarding the management of ARVD is conflicting. Randomized controlled trials failed to demonstrate superiority of percutaneous transluminal renal artery angioplasty (PTRA) with or without stenting in addition to standard medical therapy compared with medical therapy alone in lowering blood pressure levels or preventing adverse renal and cardiovascular outcomes in patients with ARVD, but they carried several limitations and met important criticism. Observational studies showed that PTRA is associated with future cardiorenal benefits in patients presenting with high-risk ARVD phenotypes (i.e. flash pulmonary oedema, resistant hypertension or rapid loss of kidney function). This clinical practice document, prepared by experts from the European Renal Best Practice (ERBP) board of the European Renal Association (ERA) and from the Working Group on Hypertension and the Kidney of the European Society of Hypertension (ESH), summarizes current knowledge in epidemiology, pathophysiology and diagnostic assessment of ARVD and presents, following a systematic literature review, key evidence relevant to treatment, with an aim to support clinicians in decision making and everyday management of patients with this condition.
A novel prognostic nomogram predicts premature failure of kidney allografts with IgA nephropathy recurrence
Authors: Bednarova Kamila , Mjøen Geir , Hruba Petra , Modos Istvan , Voska Ludek , Kollar Marek , Viklicky Ondrej 
Published: May 2023

ABSTRACT

Background
Recurrence of immunoglobulin A nephropathy (IgAN) limits graft survival in kidney transplantation. However, predictors of a worse outcome are poorly understood.

Methods
Among 442 kidney transplant recipients (KTRs) with IgAN, 83 (18.8%) KTRs exhibited biopsy-proven IgAN recurrence between 1994 and 2020 and were enrolled in the derivation cohort. A multivariable Cox model predicting allograft loss based on clinical data at the biopsy and a web-based nomogram were developed. The nomogram was externally validated using an independent cohort (n = 67).

Results
Patient age &lt;43 years {hazard ratio [HR] 2.20 [95% confidence interval (CI) 1.41–3.43], P &lt; .001}, female gender [HR 1.72 (95% CI 1.07–2.76), P = .026] and retransplantation status [HR 1.98 (95% CI 1.13–3.36), P = .016] were identified as independent risk factors for IgAN recurrence. Patient age &lt;43 years [HR 2.77 (95% CI 1.17–6.56), P = .02], proteinuria &gt;1 g/24 hours [HR 3.12 (95% CI 1.40–6.91), P = .005] and C4d positivity [HR 2.93 (95% CI 1.26–6.83), P = .013] were found to be associated with graft loss in patients with IgAN recurrence. A nomogram predicting graft loss was constructed based on clinical and histological variables, with a C statistic of 0.736 for the derivation cohort and 0.807 for the external validation cohort.

Conclusions
The established nomogram identified patients with recurrent IgAN at risk for premature graft loss with good predictive performance.
Anti-inflammatory pathways of kefir in murine model: a systematic review
Authors: Albuquerque Pereira Mariana de Fátima , Matias Albuini Fernanda , Gouveia Peluzio Maria do Carmo 
Published: May 2023

Abstract

Context
Kefir consumption has been associated with immune response modulation, antioxidant, and anti-inflammatory effects.

Objective
The objective of this systematic review was to investigate the role of kefir against inflammation and the main response mechanisms involved in this process in a murine model.

Data Sources
The searches were searched in the PubMed, Science Direct, and LILACS databases. Only murine model studies, according to PRISMA guidelines, published in the past 10 years were included.

Study Selection
Only articles about original and placebo-controlled experiments in murine models used to investigate the anti-inflammatory mechanisms of kefir were considered. Of the articles found, 349 were excluded according to the following criteria: duplicate articles (n = 99), off-topic title and abstract (n = 157), reviews (n = 47), studies in vitro (n = 29), and studies with humans (n = 17). In total, 23 studies were included in this review.

Data Extraction
Two independently working authors assessed the risk of bias and extracted data from the included studies.

Results
Kefir consumption had positive effects on inflammation modulation. The main mechanisms involved were the reduction of pro-inflammatory and molecular markers; reduction in inflammatory infiltrate in tissues, serum biomarkers, risk factors for chronic diseases, and parasitic infection; composition and metabolic activity change of intestinal microbiota and mycobiota; activation of humoral and cellular immunity; and modulation of oxidative stress.

Conclusions
Kefir modulates the immune system in different experimental models, among other secondary outcomes, to improve overall health. The beverage reduces inflammation through the alternation between innate, Th1, and Th2 responses, reducing levels of pro-inflammatory cytokines while increasing those of anti-inflammatory ones. In addition, it also mediates immunomodulatory and protective effects through the numerous molecular biomarkers and organic acids produced and secreted by kefir in the intestinal microbiota. The health-promoting effects attributed to kefir may help in the different treatments of inflammatory, chronic, and infectious diseases in the population.