bluuebunny/crossref_metadata_2025_split huggingface dataset:
The JASMONATE ZIM-domain–OPEN STOMATA1 cascade integrates jasmonic acid and abscisic acid signaling to regulate drought tolerance by mediating stomatal closure in poplar
Authors: Rao Shupei , Tian Yuru , Zhang Chong , Qin Yingzhi , Liu Meiqin , Niu Shihui , Li Yue , Chen Jinhuan 
Published: October 2022

Abstract
Drought, which directly affects the yield of crops and trees, is a natural stress with a profound impact on the economy. Improving water use efficiency (WUE) and drought tolerance are relatively effective strategies to alleviate drought stress. OPEN STOMATA1 (OST1), at the core of abscisic acid (ABA) signaling, can improve WUE by regulating stomatal closure and photosynthesis. Methyl jasmonate (MeJA) and ABA crosstalk is considered to be involved in the response to drought stress, but the detailed molecular mechanism is insufficiently known. Here, Populus euphratica, which naturally grows in arid and semiarid regions, was selected as the species for studying MeJA and ABA crosstalk under drought. A yeast two-hybrid assay was performed using PeOST1 as bait and a nucleus-localized factor, JASMONATE ZIM-domain protein 2 (PeJAZ2), was found to participate in MeJA signaling by interacting with PeOST1. Overexpression of PeJAZ2 in poplar notably increased water deficit tolerance and WUE in both severe and mild drought stress by regulating ABA signaling rather than ABA synthesis. Furthermore, a PeJAZ2 overexpression line was shown to have greater ABA-induced stomatal closure and hydrogen peroxide (H2O2) production. Collectively, this evidence establishes a mechanism in which PeJAZ2 acts as a positive regulator in response to drought stress via ABA-induced stomatal closure caused by H2O2 production. Our study presents a new insight into the crosstalk of ABA and jasmonic acid signaling in regulating WUE and drought stress, providing a basis of the drought tolerance mechanism of P. euphratica.
The homogeneity of chemical abundances in H ii regions of the Magellanic Clouds
Authors: Domínguez-Guzmán G , Rodríguez M , García-Rojas J , Esteban C , Toribio San Cipriano L 
Published: October 2022

ABSTRACT
We use very deep spectra obtained with the Ultraviolet-Visual Echelle Spectrograph at the Very Large Telescope to derive physical conditions and chemical abundances of four H ii regions of the Large Magellanic Cloud (LMC) and four H ii regions of the Small Magellanic Cloud (SMC). The observations cover the spectral range 3100–10400 Å with a spectral resolution of Δλ ≥ λ/11600, and we measure 95–225 emission lines in each object. We derive ionic and total abundances of O, N, S, Ne, Ar, Cl, and Fe using collisionally excited lines. We find average values of 12 + log (O/H) = 8.37 in the LMC and 8.01 in the SMC, with standard deviations of σ = 0.03 and 0.02 dex, respectively. The S/O, Ne/O, Ar/O, and Cl/O abundance ratios are very similar in both clouds with σ = 0.02–0.03 dex, which indicates that the chemical elements are well mixed in the interstellar medium of each galaxy. The LMC is enhanced in N/O by ∼0.20 dex with respect to the SMC, and the dispersions in N/O, σ = 0.05 dex in each cloud, are larger than those found for the other elements. The derived standard deviations would be much larger for all the abundance ratios, up to 0.20 dex for N/O, if previous spectra of these objects were used to perform the analysis. Finally, we find a wide range of iron depletions in both clouds with more than 90 per cent of the iron atoms deposited on to dust grains in most objects.
Chemical evolution of 26Al and 60Fe in the Milky Way
Authors: Vasini A , Matteucci F , Spitoni E 
Published: October 2022

ABSTRACT
We present theoretical mass estimates of 26Al and 60Fe throughout the Galaxy, performed with a numerical chemical evolution model including detailed nucleosynthesis prescriptions for stable and radioactive nuclides. We compared the results for several sets of stellar yields taken from the literature, for massive, low and intermediate mass stars, nova systems (only for 26Al) and supernovae Type Ia. We then computed the total masses of 26Al and 60Fe in the Galaxy. We studied the bulge and the disc of the Galaxy in a Galactocentric radius range of 0–22 kpc. We assumed that the bulge region (within 2 kpc) evolved quickly suffering a strong star formation burst, while the disc formed more slowly and inside–out. We compared our results with the 26Al mass observed by the gamma-ray surveys COMPTEL and INTEGRAL to select the best model. Concerning 60Fe, we do not have any observed mass value so we just performed a theoretical prediction for future observations. In conclusion, low, intermediate mass stars, and Type Ia supernovae contribute negligibly to the two isotopes, while massive stars are the dominant source. The nova contribution is, however, necessary to reproduce the observations of 26Al. Our best model predicts 2.12 M⊙ of 26Al, in agreement with observations, while for 60Fe our best mass estimate is ∼1.05 M⊙. We also predicted the present injection rate of 26Al and 60Fe in the Galaxy and compared it with previous results, and we found a larger present time injection rate along the disc.
Long-term trends of light pollution assessed from SQM measurements and an empirical atmospheric model
Authors: Puschnig Johannes , Wallner Stefan , Schwope Axel , Näslund Magnus 
Published: October 2022

ABSTRACT
We present long-term (4–10 yr) trends of light pollution observed at 26 locations, covering rural, intermediate, and urban sites, including the three major European metropolitan areas of Stockholm, Berlin, and Vienna. Our analysis is based on (i) night sky brightness (NSB) measurements obtained with sky quality metres (SQMs) and (ii) a rich set of atmospheric data products. We describe the SQM data reduction routine in which we filter for moon- and clear-sky data and correct for the SQM ‘aging’ effect using an updated version of the twilight method of Puschnig et al. (2021). Our clear-sky, aging-corrected data reveal short- and long-term (seasonal) variations due to atmospheric changes. To assess long-term anthropogenic NSB trends, we establish an empirical atmospheric model via multivariate penalized linear regression. Our modelling approach allows to quantitatively investigate the importance of different atmospheric parameters, revealing that surface albedo and vegetation have by far the largest impact on zenithal NSB. Additionally, the NSB is sensitive to black carbon and organic matter aerosols at urban and rural sites, respectively. Snow depth was found to be important for some sites, while the total column of ozone leaves impact on some rural places. The average increase in light pollution at our 11 rural sites is 1.7 per cent per year. At our nine urban sites, we measure an increase of 1.8 per cent per year and for the remaining six intermediate sites we find an average increase of 3.7 per cent per year. These numbers correspond to doubling times of 41, 39, and 19 yr. We estimate that our method is capable of detecting trend slopes shallower/steeper than ±1.5 per cent per year.
First detection of the He i 10 830 Å emission in spectra of classical Cepheid X Cyg
Authors: Kovtyukh V V , Andrievsky S M , Korotin S A 
Published: October 2022

ABSTRACT
For the first time, we describe a detection of the emission in the infrared (IR) He i triplet at 10 830 Å in the classical Cepheid X Cyg. Emissions are clearly seen at phases approximately from 0.25 to 0.85. The IR redshifted He i emission is excited by shock wave in the uppermost layers of the star’s envelope, in its falling layers. This is a first detection of the helium IR emission in the classical Cepheids.
Early Nitrogenase Ancestors Encompassed Novel Active Site Diversity
Authors: Schwartz Sarah L , Garcia Amanda K , Kaçar Betül , Fournier Gregory P 
Published: October 2022

Abstract
Ancestral sequence reconstruction (ASR) infers predicted ancestral states for sites within sequences and can constrain the functions and properties of ancestors of extant protein families. Here, we compare the likely sequences of inferred nitrogenase ancestors to extant nitrogenase sequence diversity. We show that the most-likely combinations of ancestral states for key substrate channel residues are not represented in extant sequence space, and rarely found within a more broadly defined physiochemical space—supporting that the earliest ancestors of extant nitrogenases likely had alternative substrate channel composition. These differences may indicate differing environmental selection pressures acting on nitrogenase substrate specificity in ancient environments. These results highlight ASR's potential as an in silico tool for developing hypotheses about ancestral enzyme functions, as well as improving hypothesis testing through more targeted in vitro and in vivo experiments.
Beyond corrosion: development of a single cell-ICP-ToF-MS method to uncover the process of microbiologically influenced corrosion
Authors: Olbrich Adelina-Elisa , Stepec Biwen A An , Wurzler Nina , Terol Estela C , Koerdt Andrea , Meermann Björn 
Published: October 2022

Abstract
The development of the microbiologically influenced corrosion (MIC)-specific inductively coupled plasma-time of flight-mass spectrometry (ICP-ToF-MS) analytical method presented here, in combination with the investigation of steel-MIC interactions, contributes significantly to progress in instrumental MIC analysis. For this, a MIC-specific staining procedure was developed, which ensures the analysis of intact cells. It allows the analysis of archaea at a single cell level, which is extremely scarce compared to other well-characterized organisms. The detection method revealed elemental selectivity for the corrosive methanogenic strain Methanobacterium-affiliated IM1. Hence, the possible uptake of individual elements from different steel samples was investigated and results showed the cells responded at a single-cell level to the different types of supplemented elements and displayed the abilities to uptake chromium, vanadium, titanium, cobalt, and molybdenum from solid metal surfaces. The methods developed and information obtained will be used in the future to elucidate underlying mechanisms, compliment well-developed methods, such as SEM-EDS, and develop novel material protection concepts.
Structure-based screening for functional non-coding RNAs in fission yeast identifies a factor repressing untimely initiation of sexual differentiation
Authors: Ono Yu , Katayama Kenta , Onuma Tomoki , Kubo Kento , Tsuyuzaki Hayato , Hamada Michiaki , Sato Masamitsu 
Published: October 2022

Abstract
Non-coding RNAs (ncRNAs) ubiquitously exist in normal and cancer cells. Despite their prevalent distribution, the functions of most long ncRNAs remain uncharacterized. The fission yeast Schizosaccharomyces pombe expresses &gt;1800 ncRNAs annotated to date, but most unconventional ncRNAs (excluding tRNA, rRNA, snRNA and snoRNA) remain uncharacterized. To discover the functional ncRNAs, here we performed a combinatory screening of computational and biological tests. First, all S. pombe ncRNAs were screened in silico for those showing conservation in sequence as well as in secondary structure with ncRNAs in closely related species. Almost a half of the 151 selected conserved ncRNA genes were uncharacterized. Twelve ncRNA genes that did not overlap with protein-coding sequences were next chosen for biological screening that examines defects in growth or sexual differentiation, as well as sensitivities to drugs and stresses. Finally, we highlighted an ncRNA transcribed from SPNCRNA.1669, which inhibited untimely initiation of sexual differentiation. A domain that was predicted as conserved secondary structure by the computational operations was essential for the ncRNA to function. Thus, this study demonstrates that in silico selection focusing on conservation of the secondary structure over species is a powerful method to pinpoint novel functional ncRNAs.
A phage weaponizes a satellite recombinase to subvert viral restriction
Authors: Nguyen Maria H T , Netter Zoe , Angermeyer Angus , Seed Kimberley D 
Published: October 2022

Abstract
Bacteria can acquire mobile genetic elements (MGEs) to combat infection by viruses (phages). Satellite viruses, including the PLEs (phage-inducible chromosomal island-like elements) in epidemic Vibrio cholerae, are MGEs that restrict phage replication to the benefit of their host bacterium. PLEs parasitize the lytic phage ICP1, unleashing multiple mechanisms to restrict phage replication and promote their own spread. In the arms race against PLE, ICP1 uses nucleases, including CRISPR-Cas, to destroy PLE’s genome during infection. However, through an unknown CRISPR-independent mechanism, specific ICP1 isolates subvert restriction by PLE. Here, we discover ICP1-encoded Adi that counteracts PLE by exploiting the PLE’s large serine recombinase (LSR), which normally mobilizes PLE in response to ICP1 infection. Unlike previously characterized ICP1-encoded anti-PLE mechanisms, Adi is not a nuclease itself but instead appears to modulate the activity of the LSR to promote destructive nuclease activity at the LSR’s specific attachment site, attP. The PLE LSR, its catalytic activity, and attP are additionally sufficient to sensitize a PLE encoding a resistant variant of the recombination module to Adi activity. This work highlights a unique type of adaptation arising from inter-genome conflicts, in which the intended activity of a protein can be weaponized to overcome the antagonizing genome.
Role of NS2 specific RNA binding and phosphorylation in liquid–liquid phase separation and virus assembly
Authors: Rahman Shah Kamranur , Ampah Khamal Kwesi , Roy Polly 
Published: October 2022

Abstract
Liquid–liquid phase separation (LLPS) has assumed a prominent role in biological cell systems, where it underpins the formation of subcellular compartments necessary for cell function. We investigated the underlying mechanism of LLPS in virus infected cells, where virus inclusion bodies are formed by an RNA-binding phosphoprotein (NS2) of Bluetongue virus to serve as sites for subviral particle assembly and virus maturation. We show that NS2 undergoes LLPS that is dependent on protein phosphorylation and RNA-binding and that LLPS occurrence is accompanied by a change in protein secondary structure. Site-directed mutagenesis identified two critical arginine residues in NS2 responsible for specific RNA binding and thus for NS2–RNA complex driven LLPS. Reverse genetics identified the same residues as essential for VIB assembly in infected cells and virus viability. Our findings suggest that a specific arginine–RNA interaction in the context of a phosphorylated state drives LLPS in this, and possibly other, virus infections.
Effects of Mantle Hybridization by Interaction with Slab Derived Melts in the Genesis of Alkaline Lavas across the Back-Arc Region of South Shetland Subduction System
Authors: Altunkaynak Şafak , Aldanmaz Ercan , Nývlt Daniel 
Published: October 2022

AbstractLate Miocene to Late Pleistocene alkaline lavas in the northernmost part of the Antarctic Peninsula and its off-lying islands are the latest stage of magmatic activity that took place in response to lithospheric extension in the back-arc region of the South Shetland subduction system. The alkaline magmatism occurred much later than the main pulse of Cretaceous arc magmatism and generated basaltic extrusive rocks during several sub-aqueous/sub-glacial and sub-aerial eruption periods. The suite consists primarily of alkali olivine basalts with oceanic island basalt (OIB)-like trace element signatures, characterized by elevated highly to less incompatible element ratios compared to MORB. The samples have higher 87Sr/86Sr (0.70301–0.70365), and lower 143Nd/144Nd (0.51283–0.51294) and 176Hf/177Hf (0.28291–0.28298) than depleted MORB mantle. Their lead isotope ratios vary within a limited range with 206Pb/204Pb, 207Pb/204Pb, 208Pb/204Pb ratios of 18.797–18.953, 15.577–15.634, and 38.414–38.701, respectively. Sr, Nd, Hf and Pb isotope systematics suggest involvement of diverse source materials in the genesis of the alkaline magmas. Evaluation of radiogenic isotope and trace element data indicates that the source of the alkaline melts had a complex petrogenetic history, reflecting the effects of mantle hybridization along the slab mantle interface through interaction of mantle wedge peridotites with volatile-bearing, siliceous melts produced by melting of subducted sediments and basaltic oceanic crust. Hf-Nd isotope and trace element projections further demonstrate that the metasomatizing melt was likely generated by eclogite partial melting at sub-arc to post-arc depths, in equilibrium with a garnet-bearing residue and involved breakdown of high field strength elements (HFSE) retaining phases. Consumption of metasomatic amphibole during partial melting of hybridized peridotite at the wet solidus appears to have had a significant effect on the final melt compositions with high HFSE, Na and H2O contents.
Placebos in Schizophrenia Research: An Historical Overview and Introduction to Ethical Issues
Authors: Berkhout Suze G 
Published: October 2022

Abstract
This short introduction provides a historical and ethical overview of placebos and placebo controls in relation to schizophrenia research, with a focus on long-term clinical trials. Drawing on historical and philosophical scholarship, it sketches a two-level analysis of ethical issues that placebos and the placebo effect raise for the field, particularly in light of shifts in clinical trial methodologies and clinical practices.
A machine learning eye movement detection algorithm using electrooculography
Authors: Dupre Alicia E , Cronin Michael F M , Schmugge Stephen , Tate Samuel , Wack Audrey , Prescott Brenton R , Li Cheyi , Auerbach Sanford , Suchdev Kushak , Al-Faraj Abrar , He Wei , Cervantes-Arslanian Anna M , Abdennadher Myriam , Saxena Aneeta , Lehan Walter , Russo Mary , Pugsley Brian , Greer David , Shin Min , Ong Charlene J 
Published: October 2022

AbstractStudy ObjectivesEye movement quantification in polysomnograms (PSG) is difficult and resource intensive. Automated eye movement detection would enable further study of eye movement patterns in normal and abnormal sleep, which could be clinically diagnostic of neurologic disorders, or used to monitor potential treatments. We trained a long short-term memory (LSTM) algorithm that can identify eye movement occurrence with high sensitivity and specificity.MethodsWe conducted a retrospective, single-center study using one-hour PSG samples from 47 patients 18–90 years of age. Team members manually identified and trained an LSTM algorithm to detect eye movement presence, direction, and speed. We performed a 5-fold cross validation and implemented a “fuzzy” evaluation method to account for misclassification in the preceding and subsequent 1-second of gold standard manually labeled eye movements. We assessed G-means, discrimination, sensitivity, and specificity.ResultsOverall, eye movements occurred in 9.4% of the analyzed EOG recording time from 47 patients. Eye movements were present 3.2% of N2 (lighter stages of sleep) time, 2.9% of N3 (deep sleep), and 19.8% of REM sleep. Our LSTM model had average sensitivity of 0.88 and specificity of 0.89 in 5-fold cross validation, which improved to 0.93 and 0.92 respectively using the fuzzy evaluation scheme.ConclusionAn automated algorithm can detect eye movements from EOG with excellent sensitivity and specificity. Noninvasive, automated eye movement detection has several potential clinical implications in improving sleep study stage classification and establishing normal eye movement distributions in healthy and unhealthy sleep, and in patients with and without brain injury.
Profiling transcriptional heterogeneity of epithelium, fibroblasts, and immune cells in esophageal squamous cell carcinoma by single‐cell RNA sequencing
Authors: Shi Ke , Li Yueqi , Yang Liang , Zhang Zichao , Guo Dan , Zhang Jinzhong , Lu Yucheng 
Published: October 2022

AbstractEsophageal squamous cell carcinoma (ESCC) is one of the most aggressive malignancies with complex tumor microenvironment (TME) which has been proven to be associated with therapeutic failure or resistance. A deeper understanding of the complex TME and cellular heterogeneity is urgently needed in ESCC. Here, we generated single‐cell RNA sequencing (scRNA‐seq) of 25 796 immune and 8197 non‐immune cells from three primary tumor and paired normal samples in ESCC patients. The results revealed intratumoral and intertumoral epithelium heterogeneity and tremendously differences in tumor and normal epithelium. The infiltration of myofibroblasts, one subtype of fibroblasts, might play important roles in the progression of ESCC. We also found that some differentially expressed genes and markers in epithelium and fibroblast subtypes showed prognostic values for ESCC. Diverse cell subtypes of T cells and myeloid cells were identified, including tumor‐enriched HAVCR2+ CD4+ T cells with significantly exhausted signature. The epithelium and myeloid cells had more frequent cell–cell communication compared with epithelium and T cells. Taken together, this study provided in‐depth insights into the cellular heterogeneity of TME in ESCC and highlighted potential therapeutic targets including for immunotherapy.
Strengthening the case for intralymphatic immunotherapy
Authors: Hoffmann Hans Jürgen , Hviid-Vyff Bjarke 
Published: October 2022

Purpose of review
Intralymphatic immunotherapy (ILIT) is a promising novel method of immunotherapy, that is short and convenient, and may be very effective. Results have been varied, and efforts to unravel the real value of the treatment are ongoing. Methods used to assess the effect in clinical trials have been so varied that it is difficult to compare studies with each other.

Recent findings
Some advances have been made; the importance of injecting into the lymph node has been illustrated, and treatment with a range of medicines has proven to be successful. In meta-analyses the treatment has been shown to have no serious side effects and to be an effective short term desensitizing agent. Now it remains to be shown that ILIT also has long-term effects of tolerance. Preliminary data suggest that there is a long-term effect.

Summary
Injecting allergen directly into a lymph node strengthens the protective immune response. ILIT is safe and induces desensitization and very likely also induces tolerance. Compliance will improve compared with other treatment forms. If ILIT holds its promise, it will become an attractive option for patients with allergy.